5M5N

Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP state (based on cryo-electron microscopy experiment): the N-terminus adopts multiple conformations.


ELECTRON MICROSCOPY
Sample
microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP state
Specimen Preparation
Sample Aggregation StateHELICAL ARRAY
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles144300
Reported Resolution (Å)9.3
Resolution MethodFSC 0.5 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsAn initial homology model of S. pombe cut7 kinesin-5 motor domain based on human kinesin-5 structure (PDB 3HQD) was prepared using Modeller. The coord ...An initial homology model of S. pombe cut7 kinesin-5 motor domain based on human kinesin-5 structure (PDB 3HQD) was prepared using Modeller. The coordinates of motor bound to an alpha-beta tubulin dimer (PDB 1JFF) were rigidly fitted into the cryo-EM map using Chimera and refined by flexible fitting using Flex-EM. Structural models of loop5 and loop10 were generated using Modeller. The conformation of the neck-linker and the N-terminus were calculated using a conjugate-gradient energy minimization approach.
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)700
Maximum Defocus (nm)2600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification68000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONEMAN1
CTF CORRECTIONCTFFIND3
CTF CORRECTIONFREALIGN
MODEL FITTINGUCSF Chimera
MODEL FITTINGFlex-EM
INITIAL EULER ASSIGNMENTSPIDER
FINAL EULER ASSIGNMENTFREALIGN
RECONSTRUCTIONFREALIGN
MODEL REFINEMENTFlex-EM
MODEL REFINEMENTMODELLER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION