Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (Composite map from PHENIX)
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.996
f_angle_d
0.736
f_chiral_restr
0.045
f_plane_restr
0.006
f_bond_d
0.004
Sample
Wild-type human CFTR solubilized in digitonin and cholesterol-hemisuccinate plus T2a nanobody in the presence of 2 mM MgATP
Sample Components
Wild type human Cystic Fibrosis Transmembrane Conductance Regulator (hCFTR)
T2a nanobody
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
36856
Reported Resolution (Å)
3.86
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Real space refinement in PHENIX using default parameters with separate grouped ADPs for side chain and backbone atoms. REMARK Because of the relativel ...
Real space refinement in PHENIX using default parameters with separate grouped ADPs for side chain and backbone atoms. REMARK Because of the relatively low resolution and the anisotropy of the map corresponding to this model, it was built primarily by transferring coordinates from higher resolution structures with equivalent conformations. The model for NBD2, the transmembrane region, and the bound lipids came from a 2.98 A structure of an "NBD1less" conformation of human CFTR that has no significant density for NBD1. The model for NBD1 and T2a came from a 3.04 A structure of the standard "VShaped" conformation of human CFTR (without the internal chloride channel formed) that has the T2a nanobody bound to NBD1. The relevant portions of those two models were aligned with the density in ChimeraX and then combined with a model for the C peptide that was built directly into this map. The C peptide, which has not been assigned to a specific CFTR sequence, likely derives from either the Regulatory Insertion spanning residues 403-436 or the R Region spanning residues 638-840. No manual rebuilding was performed on the model, although a small number of protein segments and two ligands showing stereochemical strains or clashes in an initial refinement in PHENIX were subject to real space refinement in COOT. Occupancy refinement was performed on the two backbone segments that have alternative conformations in the NBD1less model (541-548 and 919-922) and also on residues 1012-1034 in CFTR and the entirety of the T2a nanobody.
