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Ternary complex of DDB1dB:CRBN:mezigdomide:SALL4(392-449)
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) ...
UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
539282
Reported Resolution (Å)
2.7
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Particles were re-extracted at 1.10 A/pixel, and subsequently processed by reference-based motion correction, local CTF refinement (per-particle defoc ...
Particles were re-extracted at 1.10 A/pixel, and subsequently processed by reference-based motion correction, local CTF refinement (per-particle defocus), and global CTF refinement (per-group beam tilt and trefoil). Homogeneous refinement of these processed particles followed by local refinement with a mask encompassing the full particle yielded a final reconstruction at 2.7 A. A local refinement using a mask encompassing the CRBN:drug:ZF portion further improved drug and ZF density.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (8TNQ, 8TNQ, 8U17, 8D7Z)
Refinement Space
REAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Sharpened and unsharpened maps processed by cryoSPARC, in addition to maps post-processed with DeepEMhancer (v0.16), were used for model building. Mod ...
Sharpened and unsharpened maps processed by cryoSPARC, in addition to maps post-processed with DeepEMhancer (v0.16), were used for model building. Models of DDB1dB:CRBN (PDB: 8TNQ) and SALL4(ZF3) (PDB: 8U17) were fit into the density as individual chains using ChimeraX (v1.6.1). Mezigdomide from a model of DDB1:CRBN:mezigdomide:IKZF1(ZF1-3) (PDB: 8D7Z) was added after aligning both models on CRBN, and residues outside of SALL4(ZF3) were built using Coot (v0.9.8). A ligand restraint file for mezigdomide was generated using the Grade2 (v1.6.0), and the entire model was then relaxed into the density using Rosetta (v3.13) followed by manual adjustment in Coot. The model was prepared for refinement using phenix.ready_set (v1.21-5207) and refined using phenix.real_space_refine (v1.21-5207).
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
51.7
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
TFS TALOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2000
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
36000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
Topaz
0.2.5
IMAGE ACQUISITION
SerialEM
4.1b
CTF CORRECTION
cryoSPARC
4.2.0
MODEL FITTING
UCSF ChimeraX
1.6.1
INITIAL EULER ASSIGNMENT
cryoSPARC
4.2.0
FINAL EULER ASSIGNMENT
cryoSPARC
4.2.0
CLASSIFICATION
cryoSPARC
4.2.0
RECONSTRUCTION
cryoSPARC
4.2.0
MODEL REFINEMENT
PHENIX
1.21-5207
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
3386439
Particles were picked using Topaz (v0.2.5) trained on templates from on-the-fly 2D classification