9DUR | pdb_00009dur

Cryo-EM Structure of CRBN:dHTC1:ENL YEATS

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8TNQ
experimental model	PDB	6PHY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	4.9003
f_angle_d	0.7123
f_chiral_restr	0.0463
f_plane_restr	0.0054
f_bond_d	0.0032

Sample
Ternary complex of dHTC1 induced DDB1dB/CRBN, ENL YEATS complex
Sample Components
ENL YEATS domain
DDB1dB/CRBN

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agno ...	Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. 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 mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	185312
Reported Resolution (Å)	2.9
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8tnq, 6phy)
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value	119.8
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)
Electron Dose (electrons/Å**2)	52

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
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	165000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Topaz	0.2.5a
IMAGE ACQUISITION	EPU	3.7
CTF CORRECTION	cryoSPARC	4.5.3
MODEL FITTING	ISOLDE	1.6.0
MODEL FITTING	Coot	0.9.8.0
MODEL FITTING	UCSF ChimeraX	1.6.1
MODEL FITTING	Rosetta	3.13
INITIAL EULER ASSIGNMENT	cryoSPARC	4.5.3
FINAL EULER ASSIGNMENT	cryoSPARC	4.5.3
CLASSIFICATION	cryoSPARC	4.5.3
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.19.2-4158

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		9955887

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.