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Cryo-EM structure of murine Thrombopoietin receptor ectodomain in complex with Tpo
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
9.94
f_angle_d
0.728
f_chiral_restr
0.044
f_plane_restr
0.006
f_bond_d
0.004
Sample
2:1 complex of the mouse thrombopoietin receptor ectodomain and mouse thrombopoietin
Sample Components
mouse thrombopoietin receptor ectodomain
mouse thrombopoietin
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blot time of 4 s, blot force of 6 and no wait time or drain time.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
745000
Reported Resolution (Å)
3.6
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Final map was generated using Non-uniform refinement followed by 3DFlex refinement in cryoSPARC. Map was sharpened by deepEMhancer.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
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
ChimeraX was used to perform rigid-body fitting of domains and modelling was performed using Coot and ISOLDE. Refinement was carried out in PHENIX.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)
50.57
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
400
Maximum Defocus (nm)
3600
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
130000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.2.1
IMAGE ACQUISITION
EPU
2
CTF CORRECTION
cryoSPARC
4.2.1
MODEL FITTING
ISOLDE
1.6.0
MODEL FITTING
UCSF ChimeraX
1.6.1
MODEL FITTING
Coot
0.9.8.3
INITIAL EULER ASSIGNMENT
cryoSPARC
4.2.1
FINAL EULER ASSIGNMENT
cryoSPARC
4.2.1
CLASSIFICATION
cryoSPARC
4.2.1
RECONSTRUCTION
cryoSPARC
4.2.1
MODEL REFINEMENT
PHENIX
1.20.1_4487
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
NONE
Defocus values were estimated using patch CTF estimation and CTF correction was performed during 3D reccnstruction.
2353523
Templates for picking were generated using a gaussian based picking approach, followed by 2D classification and selection of high-quality 2D classes for template picking.