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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
5M5N
pdb_00005m5n
10.2210/pdb5m5n/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
microtubule-bound S. pombe kinesin-5 motor domain in the AMPPNP state
Specimen Preperation
Sample Aggregation State
HELICAL ARRAY
Vitrification Instrument
FEI VITROBOT MARK I
Cryogen Name
ETHANE
Sample Vitrification Details
?
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
144300
Reported Resolution (Å)
9.3
Resolution Method
FSC 0.5 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation coefficient
Overall B Value
?
Fitting Procedure
?
Details
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 Type
GATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å
2
)
20
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
700
Maximum Defocus (nm)
2600
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN CT3500 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
?
Calibrated Magnification
68000
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
EMAN
1
CTF CORRECTION
CTFFIND
3
CTF CORRECTION
FREALIGN
?
MODEL FITTING
UCSF Chimera
?
MODEL FITTING
Flex-EM
?
INITIAL EULER ASSIGNMENT
SPIDER
?
FINAL EULER ASSIGNMENT
FREALIGN
?
RECONSTRUCTION
FREALIGN
?
MODEL REFINEMENT
Flex-EM
?
MODEL REFINEMENT
MODELLER
?
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
