Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Cryo-EM structure of Kip3 (AMPPNP) bound to GMPCPP-Stabilized Microtubules
Sample Components
GMPCPP-stabilized microtubules
yeast kinesin-8/ Kip3
Specimen Preparation
Sample Aggregation State
HELICAL ARRAY
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
21788
Reported Resolution (Å)
4.1
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C14
Axial Rise
8.9
Angular Rotation
-25.76
Map-Model Fitting and Refinement
Id
1 (3JAT, 3JAT, 4FRZ)
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall correlation of the residues to the map
Overall B Value
100
Fitting Procedure
Details
Multiple rounds of refinement were carried out against one half map (training map), and the other half map (validation map) was used to monitor overfi ...
Multiple rounds of refinement were carried out against one half map (training map), and the other half map (validation map) was used to monitor overfitting based on the procedure described in Wang et al. elife, 2016. It is to note that the molecular interactions of ligand-protein were restrained to the initial poses adapted from the high-resolution structures during structure refinement.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
40
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI POLARA 300
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Images were recorded using a semi-automated acquisition program Serial EM with a defocus range from 1.5 to 3.5 um.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
Appion
CTF CORRECTION
CTFFIND
4
MODEL FITTING
Rosetta
MODEL REFINEMENT
Rosetta
INITIAL EULER ASSIGNMENT
EMAN2
FINAL EULER ASSIGNMENT
FREALIGN
RECONSTRUCTION
FREALIGN
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
The contrast transfer function (CTF) was estimated using CTFFIND4 [(Rohou and Grigorieff, 2015) CTFFIND4: Fast and accurate] with a 500 um step search. A second CTFFIND run with a 100 um step search was carried out to refine the initial defocus values. Micrographs whose estimated resolution was lower than 8 Angstrom with 0.8 confidence were excluded.
29090
Inspection, defocus estimation, microtubule picking, and stack creation were performed within the Appion processing environment (Lander et al., 2009). Images were selected for processing on the basis of high decoration, straight MTs, and the absence of crystalline ice.