8RQC

Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2

• PDB DOI: https://doi.org/10.2210/pdb8RQC/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-17 Released: 2024-09-25 
• Deposition Author(s): Furihata, H., Kroupova, A., Zollman, D., Ciulli, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.286 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 

Starting Model: experimental

Literature

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

Kroupova, A., Spiteri, V., Furihata, H., Darren, D., Ramachandran, S., Rutter, Z., Chakraborti, S., Haubrich, K., Pethe, J., Gonzales, D., Wijaya, A., Rodriguez-Rios, M., Lynch, D., Farnaby, W., Nakasone, M., Zollman, D., Ciulli, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 84.39 kDa 
• Atom Count: 5,303 
• Modelled Residue Count: 666 
• Deposited Residue Count: 730 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, C [auth D]	329	Homo sapiens	Mutation(s): 12  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2 GTEx:  ENSG00000113851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein Ikaros	B, D [auth E]	36	Homo sapiens	Mutation(s): 0  Gene Names: IKZF1, IK1, IKAROS, LYF1, ZNFN1A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13422 (Homo sapiens) Explore Q13422  Go to UniProtKB:  Q13422
PHAROS:  Q13422 GTEx:  ENSG00000185811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QFC (Subject of Investigation/LOI)	F [auth A], I [auth D]	Mezigdomide C32 H30 F N5 O4 YTINZZFBHWSAGL-NDEPHWFRSA-N
ZN	E [auth A], G [auth B], H [auth D], J [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.286 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.585	α = 90
b = 142.842	β = 112.341
c = 56.693	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
Coot	model building
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Furihata, H., Kroupova, A., Zollman, D., Ciulli, A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release