9OS2 | pdb_00009os2

Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex

• PDB DOI: https://doi.org/10.2210/pdb9OS2/pdb
• EM Map EMD-70791: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-23 Released: 2026-01-28 
• Deposition Author(s): Quan, C., Petzold, G., Gainza, P., Tsai, J., Bunker, R.D., Wiedmer, L., Donckele, E.J.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry

Annunziato, S., Quan, C., Donckele, E.J., Lamberto, I., Bunker, R.D., Zlotosch, M., Schwander, L., Murthy, A., Wiedmer, L., Staehly, C., Matysik, M., Gilberto, S., Kapsitidou, D., Wible, D., de Donatis, G.D., Trenh, P., SriRamaratnam, R., Strande, V., Almeida, R., Dolgikh, E., DeMarco, B., Tsai, J., Sadok, A., Zarayskiy, V., Walter, M., Tiedt, R., Lumb, K.J., Bonenfant, D., Fasching, B., Castle, J.C., Townson, S.A., Petzold, G., Gainza, P.

(2026) Nat Struct Mol Biol 

• DOI: https://doi.org/10.1038/s41594-025-01738-8

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 279.73 kDa 
• Atom Count: 11,132 
• Modeled Residue Count: 1,407 
• Deposited Residue Count: 2,482 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A [auth B]	378	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	B [auth A]	1,140	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras GTPase-activating protein-binding protein 2	C, D	482	Homo sapiens	Mutation(s): 0  Gene Names: G3BP2, KIAA0660
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN86 (Homo sapiens) Explore Q9UN86  Go to UniProtKB:  Q9UN86
PHAROS:  Q9UN86 GTEx:  ENSG00000138757

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CED (Subject of Investigation/LOI)	F [auth B]	(1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide C30 H29 Cl N6 O5 S WXNMJKWQBTVEPQ-DFBJGRDBSA-N
ZN	E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Quan, C., Petzold, G., Gainza, P., Tsai, J., Bunker, R.D., Wiedmer, L., Donckele, E.J.

---

Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release