ELECTRON MICROSCOPY

Sample

Ternary complex of DDB1dB:CRBN:mezigdomide:SALL4(392-449)

Specimen Preperation
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) 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 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
Map-Model Fitting and Refinement
ID 1
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. 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/Å2) 51.7
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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 ?
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