Cryo EM structure of the E. coli disaggregase ClpB (BAP form, DWB mutant), in the ATPgammaS state, bound to the model substrate casein
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
6.985
f_angle_d
1.112
f_chiral_restr
0.058
f_bond_d
0.008
f_plane_restr
0.008
Sample
ClpB, BAP form, double walker B mutant
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
230000
Reported Resolution (Å)
4.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Local correlation coefficient
Overall B Value
Fitting Procedure
Details
Initial models of the monomer were generated using MODELLER v9.17 with previously determined crystal structures of ClpB or ClpB domains as templates ( ...
Initial models of the monomer were generated using MODELLER v9.17 with previously determined crystal structures of ClpB or ClpB domains as templates (PDB ids 4CIU, 1QVR, 4HSE and 4LJ9). The crystal structure of E. coli ClpB (4CIU) was used as a main template, the crystal structure of T. thermophilus (1QVR) was used to model positions of the NTD and the crystal structures of AAA1 and AAA2 of E. coli ClpB (4HSE and 4LJ9) were used to model the pore loops disordered in other crystal structures. Initial rigid body fitting of the monomers in the map was manually done in Chimera using the Fit-in-Map tool.
iMODFIT was used for fitting involving large domain motions. FlexEM was then used for refinement of secondary structures and loops in the map. Quality and improvement of the fit was assessed with TEMPy using the Segment based Manders Overlap Coefficient (SMOC) scores and segment based cross correlation scores. Ridig body fitting of ATPgammaS (structure extracted from PDB id 3EIH) into the nucleotide biding sides was manually done in Chimera using the Fit-in-Map tool. The target map for fitting of ATPgammaS was the difference map between experimental map and map generated using the nucleotide-free protein model revealing nucleotide densities. A round of real-space refinement was performed in phenix using energy minimization to fix the model's geometry and clashes.
