3J8Y

High-resolution structure of ATP analog-bound kinesin on microtubules


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HNA 
Sample
Microtubule decorated with monomeric human kinesin (K349 construct) having ADP aluminum fluoride complex bound in the nucleotide pocket
Sample Components
Human monomeric kinesin-1A construct
Alpha-tubulin
Beta-tubulin
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsNo glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequentl ...No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were performed with ~0.5 second delay after blotting but prior to plunging into liquid ethane.
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles49961
Reported Resolution (Å)5
Resolution MethodFSC 0.143 CUT-OFF
Other DetailsInitial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement were done by FREALIGN.
Refinement Type
Symmetry TypeHELICAL
Axial SymmetryC1
Axial Rise8.5215
Angular Rotation25.77
Map-Model Fitting and Refinement
Id1 (4HNA, 4HNA, 4HNA)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetRMSD from the starting structure was monitored for convergence.
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation, after placing active-site water coordinates identified in high-r ...REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation, after placing active-site water coordinates identified in high-resolution crystal structures of kinesins ATP-like state. Side chains were excluded from the MDFF target potential. Following several equilibration steps, the relative strength of the EM map potential (GSCALE term) was slowly increased from 0 to 1 over the course of 10 nanoseconds. The t = 1.4 ns time point was selected to represent the final fitted model, based on the approximate convergence of the RMSD from the starting structure.
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)15
Imaging Experiment1
Date of Experiment2013-06-02
Temperature (Kelvin)
Microscope ModelFEI TITAN
Minimum Defocus (nm)1000
Maximum Defocus (nm)2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification
Calibrated Magnification23859
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details4K x 4K counting mode was used. 24 frames total were collected.
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
RECONSTRUCTIONFREALIGN
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
done within FREALIGN