8TNP

Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FQD 
experimental modelPDB 8G46 
experimental modelPDB 6H0F 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.8878
f_angle_d0.5479
f_chiral_restr0.045
f_bond_d0.0045
f_plane_restr0.0038
Sample
Ternary Complex of DDB1dB:CRBN:pomalidomide with SD40
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification DetailsLeica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic ...Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles55205
Reported Resolution (Å)3.3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (5FQD, 8G46, 6H0F)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetCC
Overall B Value102
Fitting Procedure
DetailsPhenix real-space refinement without rigid body
Data Acquisition
Detector TypeGATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)53.8
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS TALOS
Minimum Defocus (nm)800
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification36000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONTopaz0.2.5
IMAGE ACQUISITIONSerialEM4.1b
CTF CORRECTIONcryoSPARC4.2.0
MODEL FITTINGUCSF ChimeraX1.5
INITIAL EULER ASSIGNMENTcryoSPARC4.2.0
FINAL EULER ASSIGNMENTcryoSPARC4.2.0
CLASSIFICATIONcryoSPARC4.2.0
RECONSTRUCTIONcryoSPARC4.2.0
MODEL REFINEMENTPHENIX1.19.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1254659