8OID

Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8A2T 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.0453
f_angle_d0.5764
f_chiral_restr0.0441
f_plane_restr0.0041
f_bond_d0.0037
Sample
Actin filament harboring the N111S mutation.
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE-PROPANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles1756928
Reported Resolution (Å)2.3
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsThe final refinement was performed from local searches in RELION.
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Detailschain 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 TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)70
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification130000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging DetailsTitan Krios G3 microscope was aligned using Sherpa (FEI). Data collected in superresolution mode.
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcrYOLO1.5.8
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND4.13
MODEL FITTINGCoot0.9.8.1
INITIAL EULER ASSIGNMENTSPHIRE1.4
FINAL EULER ASSIGNMENTRELION3.1.0
CLASSIFICATIONRELION3.1.0
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.20.1-4487-000
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2001281crYOLO in filament mode.