5JLH | pdb_00005jlh

Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3J8A
experimental model	PDB	4PD3
experimental model	PDB	4A7F

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	37.636
r_long_range_B_refined	37.635
r_dihedral_angle_2_deg	27.036
r_scangle_other	22.84
r_mcangle_other	18.922
r_mcangle_it	18.921
r_scbond_it	13.206
r_scbond_other	13.204
r_dihedral_angle_3_deg	13.084
r_dihedral_angle_4_deg	11.793
r_mcbond_it	11.451
r_mcbond_other	11.444
r_dihedral_angle_1_deg	7.119
r_angle_refined_deg	1.833
r_angle_other_deg	1.155
r_chiral_restr	0.117
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
F-actin-myosin-tropomyosin complex
Sample Components
actin, myosin
tropomyosin

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	GATAN CRYOPLUNGE 3
Cryogen Name	ETHANE
Sample Vitrification Details	Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper.
Embedding Material	I
Embedding Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	118000
Reported Resolution (Å)	3.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details	THE TROPOMYOSIN MAP FILTERED TO 7.0 ANGSTROM WAS MERGED WITH THE FINAL F-ACTIN-MYOSIN MAP (3.9 ANGSTROM) TO OBTAIN A MAP OF THE ENTIRE F-ACTIN-MYOSIN-TROPOMYOSIN COMPLEX.
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	27.5
Angular Rotation	166.9

Map-Model Fitting and Refinement
Id	1 (3J8A, 4PD3, 3J8A, 3J8A, 3J8A, 3J8A)	2 (4A7F, 4A7F)
Refinement Space
Refinement Protocol	BACKBONE TRACE	RIGID BODY FIT
Refinement Target
Overall B Value	180
Fitting Procedure
Details		tropomyosin fitting

Data Acquisition
Detector Type	FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)	16

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification	59000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Cs corrected microscope

EM Software
Task	Software Package	Version
PARTICLE SELECTION	SPARX
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4
CTF CORRECTION	RELION	1.3
MODEL FITTING	MODELLER
MODEL FITTING	UCSF Chimera
MODEL FITTING	iMODFIT
MODEL REFINEMENT	Coot
MODEL REFINEMENT	REFMAC
INITIAL EULER ASSIGNMENT	RELION	1.3
FINAL EULER ASSIGNMENT	RELION	1.3
CLASSIFICATION	RELION	1.3
CLASSIFICATION	SPARX
RECONSTRUCTION	RELION	1.3

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		138000