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 10DW | pdb_000010dw

Structure of CRBN/DDB1dB-KAT2A-Compound4 ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 10DW

This is version 1.0 of the entry. See complete history. 

Literature

Degron-independent recruitment of KAT2A expands the target space of CRBN molecular glues.

Ojeda, S., Wang, M., Baek, K., Bourgeois, W., Sommerschield, A., Yue, H., Metivier, R.J., Karagiannis, P., Levitz, T.S., Xiong, Y., Donovan, K.A., Armstrong, S.A., Fischer, E.S.

(2026) Science 393: 188-194

  • DOI: https://doi.org/10.1126/science.aef5391
  • Primary Citation Related Structures: 
    10DW

  • PubMed Abstract: 

    Lysine acetyltransferases (KATs) cooperate with oncogenes such as c-Myc, estrogen receptor, and lysine methyltransferase 2A (KMT2A) fusions to sustain malignant programs. Targeting of KAT proteins has shown clinical efficacy; however, achieving homolog selectivity for most KATs remains a major challenge. By extending cereblon (CRBN)-based molecular glues beyond the canonical degron space, we developed an exquisitely selective degrader of KAT2A. Cryo-electron microscopy revealed that CRBN recruits KAT2A independently of a degron; instead, the molecular glue engages a surface-exposed tyrosine, mimicking antibody-like molecular recognition. Selective KAT2A degradation leads to potent ablation of histone H3 lysine 9 acetylation (H3K9Ac), antiproliferative effects in acute myeloid leukemia cell lines, and in vivo efficacy in a patient-derived xenograft model, establishing KAT2A as a targetable vulnerability to treat a wide range of malignancies. More generally, degron-independent recruitment extends the CRBN-targetable proteome.


  • Organizational Affiliation: 
    • Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 190.72 kDa 
  • Atom Count: 11,026 
  • Modeled Residue Count: 1,371 
  • Deposited Residue Count: 1,675 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2A331Homo sapiensMutation(s): 0 
Gene Names: KAT2A, GCN5, GCN5L2
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92830 (Homo sapiens)
Explore Q92830 
Go to UniProtKB:  Q92830
PHAROS:  Q92830
GTEx:  ENSG00000108773 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92830
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cereblonB [auth C]485Homo sapiensMutation(s): 0 
Gene Names: CRBN
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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1C [auth B]859Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesP01CA066996
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR01CA262188
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR01CA214608
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR01CA218278

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release