9HPJ | pdb_00009hpj

Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2

• PDB DOI: https://doi.org/10.2210/pdb9HPJ/pdb
• EM Map EMD-52331: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-12-13 Released: 2025-12-03 
• Deposition Author(s): Langousis, G., Hunkeler, M., Chami, M., Quan, C., Townson, S., Bonenfant, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

A degron-mimicking molecular glue drives CRBN homo-dimerization and degradation.

Langousis, G., Gainza, P., Hunkeler, M., Kapsitidou, D., Donckele, E.J., Annunziato, S., Wiedmer, L., Jones, K.F.M., DeMarco, B., Quan, C., Bunker, R.D., Lumb, K.J., Fasching, B., Castle, J.C., Townson, S.A., Bonenfant, D.

(2025) Nat Commun 16: 10157-10157

• PubMed: 41258141 
• DOI: https://doi.org/10.1038/s41467-025-65094-3
• Primary Citation Related Structures: 
  9HPI, 9HPJ


• PubMed Abstract: 
  

  Cereblon (CRBN) is an E3 ubiquitin ligase widely harnessed for targeted protein degradation (TPD). We report the discovery of a molecular glue degrader (MGD), MRT-31619, that drives homo-dimerization of CRBN and promotes its fast, potent, and selective degradation by the ubiquitin proteasome system. Interestingly, the cryo-electron microscopy (cryo-EM) structure of the CRBN homodimer reveals a unique mechanism whereby two molecular glues assemble into a helix-like structure and drive ternary complex formation by mimicking a neosubstrate G-loop degron. This CRBN chemical knockout offers a valuable tool to elucidate the molecular mechanism of MGDs, to investigate its endogenous substrates and understand their physiological roles.

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Organizational Affiliation: 
• Monte Rosa Therapeutics AG, Basel, Switzerland.
University of Basel, BioEM Lab, Basel, Switzerland.
Monte Rosa Therapeutics AG, Basel, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 186.95 kDa 
• Atom Count: 12,045 
• Modeled Residue Count: 1,499 
• Deposited Residue Count: 1,642 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	836	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, C	403	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IW1 (Subject of Investigation/LOI)	E [auth B], G [auth C]	(3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione C28 H30 N4 O4 MMJAYQPOAOAOHR-QHCPKHFHSA-N
ZN	D [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	PHENIX	1.21

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Langousis, G., Hunkeler, M., Chami, M., Quan, C., Townson, S., Bonenfant, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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