9OUK | pdb_00009ouk

DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission

• PDB DOI: https://doi.org/10.2210/pdb9OUK/pdb
• EM Map EMD-70867: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera aff. frugiperda 1 BOLD-2017, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-28 Released: 2025-12-03 
• Deposition Author(s): Rizvi, Z., Lander, G.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Identification of a cryptic allosteric site on the E3 ligase adapter protein cereblon

Rizvi, Z., Dippon, V.N., Choudhry, A.E., Chung, C.W., Alkuraya, I.F., Xu, W., Tao, X.B., Jurewicz, A.J., Schneck, J.L., Chen, W., Curnutt, N.M., Kabir, F., Chan, K.H., Queisser, M.A., Musetti, C., Dai, H., Benowitz, A.B., Woo, C.M., Lander, G.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 152.99 kDa 
• Atom Count: 9,638 
• Modeled Residue Count: 1,210 
• Deposited Residue Count: 1,350 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	844	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	B	449	Homo sapiens	Mutation(s): 0  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein Ikaros	C	57	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
A1CEK (Subject of Investigation/LOI)	E [auth B]	N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide C20 H17 N3 O4 CIVWAWPQWLUMPF-INIZCTEOSA-N
ZN	D [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	v2.0orc1-5617

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Rizvi, Z., Lander, G.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM143805

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release