3JBH

TWO HEAVY MEROMYOSIN INTERACTING-HEADS MOTIFS FLEXIBLE DOCKED INTO TARANTULA THICK FILAMENT 3D-MAP ALLOWS IN DEPTH STUDY OF INTRA- AND INTERMOLECULAR INTERACTIONS


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DTP 
Sample
Myosin filaments from Tarantula striated muscle
Sample Components
MYOSIN II
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsBlotting 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 ...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 MethodHELICAL
Number of Particles
Reported Resolution (Å)20
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsThree-dimensional single particle reconstruction was carried out by a modification of the IHRSR method, using SPIDER. Low-dose electron micrographs of ...Three-dimensional single particle reconstruction was carried out by a modification of the IHRSR method, using SPIDER. Low-dose electron micrographs of 1008 frozen-hydrated thick filaments halves ere digitized at 0.248 nm per pixel using a Nikon Super Coolscan 8000 ED scanner. Filaments were aligned with the bare zone at the top, to ensure correct polarity in subsequent steps. 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. As an initial reference model we used the tarantula negatively stained 3D-map, which was axially rotated, axially shifted and also out of plane tilted up to plus-minus12deg. for projection matching, giving a total of 4,095 projections (13 tilted projections plus-minus12deg. 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 TypeHELICAL
Axial SymmetryC4
Axial Rise100
Angular Rotation30
Map-Model Fitting and Refinement
Id1 (3DTP)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCorrelation
Overall B Value
Fitting Procedure
DetailsMETHOD--FLEXIBLE FITTING DETAILS--Protocol- Flexible Fitting. The flexible docking procedure is based on a connected (motion capture) network of ide ...METHOD--FLEXIBLE FITTING DETAILS--Protocol- Flexible Fitting. The flexible docking procedure is based on a connected (motion capture) network of identified features within the atomic model. The atomic model is allowed to move according to displacements tracked by 31 control points defined by the network, in order to find the best match to the cryo-EM map
Data Acquisition
Detector TypeKODAK SO-163 FILM
Electron Dose (electrons/Å**2)
Imaging Experiment1
Date of Experiment2002-10-23
Temperature (Kelvin)88
Microscope ModelFEI/PHILIPS CM120T
Minimum Defocus (nm)1950
Maximum Defocus (nm)1950
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification35000
Calibrated Magnification35000
SourceLAB6
Acceleration Voltage (kV)120
Imaging Detailslow dose
EM Software
TaskSoftware PackageVersion
MODEL FITTINGSitus2.3
RECONSTRUCTIONSPIDER