8OID

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

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8A2T

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.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.5.8
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4.13
MODEL FITTING	Coot	0.9.8.1
INITIAL EULER ASSIGNMENT	SPHIRE	1.4
FINAL EULER ASSIGNMENT	RELION	3.1.0
CLASSIFICATION	RELION	3.1.0
RECONSTRUCTION	RELION	3.1.0
MODEL REFINEMENT	PHENIX	1.20.1-4487-000

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2001281	crYOLO in filament mode.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.