9YA5 | pdb_00009ya5

KIF1A R350G bound to microtubules in two-heads-bound state with AMP-PNP


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8UTN 
Sample
KIF1A R350G bound to microtubules in two-heads-bound state with AMP-PNP
Sample Components
KIF1A R350G motor domain
Tubulins
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs w ...4uL of a 6uM MT solution in BRB80 (80mM PIPES, 2mM MgCl2, 1mM EGTA pH 6.8) along with 20uM paclitaxel was added onto a plasma-cleaned grid. The MTs were incubated for 1 minute at room temperature, and then the excess liquid was removed from the grid using Whatman #1 paper. Next, 4uL of a solution containing 20uM KIF1A-R350G in BRB80 supplemented with 20uM paclitaxel and 5mM AMP-PNP was added to the grid. The grid with the MT and kinesin mixture was then mounted into a Vitrobot, incubated for 1 minute at room temperature, and plunge-frozen into liquid nitrogen-cooled ethane.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles1194267
Reported Resolution (Å)2.95
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise5.453
Angular Rotation168.07
Axial SymmetryC1
Axial Rise5.453
Angular Rotation168.07
Axial SymmetryC1
Axial Rise5.453
Angular Rotation168.07
Axial SymmetryC1
Axial Rise5.453
Angular Rotation168.07
Map-Model Fitting and Refinement
Id1 (8UTN, 8UTN, 8UTN, 8UTN, 8UTN, 8UTN)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement Target
Overall B Value84.3
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)50.27
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)600
Maximum Defocus (nm)2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS0.001
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification81000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.6.0
MODEL FITTINGUCSF Chimera
MODEL FITTINGRosetta
MODEL REFINEMENTPHENIX
CLASSIFICATIONcryoSPARC4.6.0
RECONSTRUCTIONcryoSPARC4.6.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION