Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
13.0453
f_angle_d
0.5764
f_chiral_restr
0.0441
f_plane_restr
0.0041
f_bond_d
0.0037
Sample
Actin filament harboring the N111S mutation.
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
1756928
Reported Resolution (Å)
2.3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
The final refinement was performed from local searches in RELION.
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
chain C of pdb 8A2T (including all water molecules) was fit in the central actin subunit of the density map. After substitution of all alpha-actin spe ...
chain C of pdb 8A2T (including all water molecules) was fit in the central actin subunit of the density map. After substitution of all alpha-actin specific amino-acids to the corresponding beta-actin residues, introducing the N111S mutation, and further manual model building in Coot, the resulting model was fitted in four more actin subunits (chains A, B, D, E) in the density map. The filament was modeled as a pentamer to capture the full interaction interface of the central subunit with its four neighboring subunits. All water molecules were first manually built, inspected and adjusted in the central subunit, and were then copied to the other chains with non-crystallographic symmetry (NCS). Because the local resolution was worse at the periphery of the reconstruction, we removed water molecules that displayed poor corresponding cryo-EM density in the non-central actin chains. The model was refined in Phenix real-space refine with NCS restraints but without Ramachandran and rotamer restraints.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
70
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
130000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Titan Krios G3 microscope was aligned using Sherpa (FEI).
Data collected in superresolution mode.
