3J8X | pdb_00003j8x

High-resolution structure of no-nucleotide kinesin on microtubules

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HNA

Sample
Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket
Sample Components
Human monomeric kinesin-1A construct
Alpha-tubulin
Beta-tubulin

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details	No 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 Method	HELICAL
Number of Particles	120783
Reported Resolution (Å)	5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Initial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement were done by FREALIGN.
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	8.78
Angular Rotation	25.77

Map-Model Fitting and Refinement
Id	1 (4HNA, 4HNA, 4HNA)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	RMSD from the starting structure was monitored for convergence.
Overall B Value
Fitting Procedure
Details	REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation. Side chains were excluded from the MDFF target potential. Followi ...	REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation. 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 = 1.2 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 Type	GATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)	15

Imaging Experiment	1
Date of Experiment	2013-04-15
Temperature (Kelvin)
Microscope Model	FEI TECNAI F30
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	GATAN LIQUID NITROGEN
Nominal Magnification	130000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	8K x 8K super-resolution mode was used. 10 frames total were collected.

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
RECONSTRUCTION	FREALIGN
RECONSTRUCTION	SPIDER

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	done within FREALIGN

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.