9W2F | pdb_00009w2f

Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9W2F

This is version 1.2 of the entry. See complete history

Literature

Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer.

Lu, X.Wang, X.Yang, Z.Wang, X.Wang, L.Xu, C.Lo, I.C.Geng, C.Wang, L.Pu, Y.Zhang, K.Zhu, Z.Ye, L.Huang, J.Wei, X.Bai, F.Zhu, Y.Qian, X.Dou, H.Su, H.Cang, Y.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10613-5
  • Primary Citation Related Structures: 
    9W2F

  • PubMed Abstract: 

    BRAF gain-of-function mutations, particularly BRAF(V600E), affect roughly 10% of all patients with colorectal cancer (CRC), and portend poor prognosis with limited therapeutic interventions. BRAF inhibitors such as encorafenib are ineffective due to MAPK pathway reactivation driven by BRAF dimerization. Combined inhibition of BRAF and EGFR, although approved therapies, results in short survival benefits and frequent treatment resistance and relapse 1-3 . Here, through rational chemical library design coupled with parallel proteomic screening, we identified dHuR as a molecular glue degrader of human antigen R (HuR), an RNA-binding protein that drives tumour growth, invasion and therapy resistance. dHuR binds to the CRBN ubiquitin ligase to create a unique benzofuran-tethered composite surface to recruit HuR as a neosubstrate by engaging its β-hairpin G-loop degron, as revealed by the cryo-electron microscopy structure of the ternary complex. dHuR abrogated BRAF expression by inducing its exon 18 skipping, and demonstrated superior suppression of BRAF-mutant CRC tumours including those gaining resistance to BRAF inhibitors. Finally, we performed kinome library CRISPR screening and revealed that inactivation of EGFR or MEK enhanced dHuR cytotoxicity, thus establishing a combinatorial strategy to treat patients with refractory BRAF-mutant CRC.


  • Organizational Affiliation
    • School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 180.84 kDa 
  • Atom Count: 9,924 
  • Modeled Residue Count: 1,274 
  • Deposited Residue Count: 1,606 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA damage-binding protein 11,140Homo 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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein cereblon381Homo 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:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ELAV-like protein 185Homo sapiensMutation(s): 0 
Gene Names: ELAVL1HUR
UniProt & NIH Common Fund Data Resources
Find proteins for Q15717 (Homo sapiens)
Explore Q15717 
Go to UniProtKB:  Q15717
PHAROS:  Q15717
GTEx:  ENSG00000066044 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15717
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EUN
(Subject of Investigation/LOI)

Query on A1EUN



Download:Ideal Coordinates CCD File
E [auth B](3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione
C24 H21 N3 O4
JDTIPDAGINDDME-FQEVSTJZSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina2024
Ministry of Education (MoE, China)ChinaJYB2025XDXM502

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Data collection, Database references
  • Version 1.2: 2026-06-24
    Changes: Data collection, Database references