5TBY | pdb_00005tby

HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF OBTAINED BY HOMOLOGY MODELING (USING SWISS-MODEL) OF HUMAN SEQUENCE FROM APHONOPELMA HOMOLOGY MODEL (PDB-3JBH), RIGIDLY FITTED TO HUMAN BETA-CARDIAC NEGATIVELY STAINED THICK FILAMENT 3D-RECONSTRUCTION (EMD-2240)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3JBH

Sample
MYOSIN THICK FILAMENTS TARANTULA STRIATED MUSCLE

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	PLUNGING IN A LIQUID ETHANE COOLED BY LIQUID NITROGEN. BLOTTING WAS PERFORMED FROM ONE SIDE OF THE GRID TILL A THIN SAMPLE FILM ON IT USING WHATMAN NO ...	PLUNGING IN A LIQUID ETHANE COOLED BY LIQUID NITROGEN. BLOTTING WAS PERFORMED FROM ONE SIDE OF THE GRID TILL A THIN SAMPLE FILM ON IT USING WHATMAN NO. 42 FILTER PAPER, THEN THE GRID WAS IMMEDIATELY PLUNGED UNDER GRAVITY INTO LIQUID ETHANE COOLED BY LIQUID NITROGEN. GRIDS WERE STORED UNDER LIQUID NITROGEN.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	10700
Reported Resolution (Å)	20
Resolution Method	FSC 0.5 CUT-OFF
Other Details	For projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2deg., 45 reference rotated projections ( ...	For projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus 12 deg. every 2deg., 45 reference rotated projections (0-90 degrees, 2deg. rotation angle), and 7 image axial shifts of 2.2 nm. The resulting 3D-map combines about 10,700 out of 15,504 filament segments, a yield of 69 percent of included segments. There are 4 helices of myosin heads, rotated 30 degrees, every 145 Angstroms. The filament segments were selected based on visual judgement of good helical order.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C4

Map-Model Fitting and Refinement
Id	1 (3JBH, 3JBH, 3JBH, 3JBH, 3JBH, 3JBH)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target	CORRELATION COEFFICIENT
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	KODAK SO-163 FILM
Electron Dose (electrons/Å**2)	9

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI/PHILIPS CM120T
Minimum Defocus (nm)	1950
Maximum Defocus (nm)	1950
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	35000
Calibrated Magnification	35000
Source	LAB6
Acceleration Voltage (kV)	120
Imaging Details	Holey carbon grids Cryopreserved in Liquid ethane were observed in a Philips CM120 electron microscope under low dose conditions. Only filaments on thin carbon over holes were photographed

EM Software
Task	Software Package	Version
PARTICLE SELECTION	EMAN	2
MODEL FITTING	UCSF Chimera	10
RECONSTRUCTION	ITERATIVE HELICAL REAL SPACE RECONSTRUCTION (EGELMAN, 2000)	SPIDER 14

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE		15504	A total of 15,504 segments, each 62 nm long, with an overlap of 55.8 nm, and containing aprox. 40,000 unique pairs of interacting myosin heads went into the reconstruction.

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.