9OS2 | pdb_00009os2

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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.M.Trenh, P.SriRamaratnam, R.Strande, V.Lieberherr, R.Lyon, D.Steiner, D.Silva, J.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.Gainza, P.Petzold, G.

(2026) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01738-8
  • Primary Citation of Related Structures:  
    9OS2

  • PubMed Abstract: 

    Molecular glue degraders (MGDs) are small-molecule compounds that divert E3 ligases to degrade nonnatural substrates called neosubstrates. Clinically effective MGDs bind cereblon (CRBN), a substrate receptor of the Cullin 4-RING E3 ubiquitin ligase (CRL4 CRBN ), and recruit neosubstrates to an MGD-induced neosurface on the CRBN CULT domain through molecular mimicry of a natural CRBN degron. Here, we identify G3BP2 (Ras-GAP SH3 domain-binding protein 2), a neosubstrate that bypasses canonical interactions with CRBN by engaging an unconventional binding site on the CRBN LON domain. The ternary complex interface does not resemble known interactions with CRBN. Instead, CRBN leverages a preexisting protein-protein interaction (PPI) hotspot on the target protein by mimicking an endogenous binding partner of G3BP2. Our findings suggest that composite neosurfaces that mimic and stabilize the footprint of natural PPIs (in short, 'glueprints') could become a viable strategy for the rational expansion of the MGD target repertoire.


  • Organizational Affiliation
    • Monte Rosa Therapeutics, Inc., Boston, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblonA [auth B]378Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1B [auth A]1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ras GTPase-activating protein-binding protein 2
C, D
482Homo sapiensMutation(s): 0 
Gene Names: G3BP2KIAA0660
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN86 (Homo sapiens)
Explore Q9UN86 
Go to UniProtKB:  Q9UN86
PHAROS:  Q9UN86
GTEx:  ENSG00000138757 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UN86
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CED (Subject of Investigation/LOI)
Query on A1CED

Download Ideal Coordinates CCD File 
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
Query on ZN

Download Ideal Coordinates CCD File 
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:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-28
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references