8TL6

Cryo-EM structure of DDB1deltaB-DDA1-DCAF5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 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

Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF.

Radko-Juettner, S.Yue, H.Myers, J.A.Carter, R.D.Robertson, A.N.Mittal, P.Zhu, Z.Hansen, B.S.Donovan, K.A.Hunkeler, M.Rosikiewicz, W.Wu, Z.McReynolds, M.G.Roy Burman, S.S.Schmoker, A.M.Mageed, N.Brown, S.A.Mobley, R.J.Partridge, J.F.Stewart, E.A.Pruett-Miller, S.M.Nabet, B.Peng, J.Gray, N.S.Fischer, E.S.Roberts, C.W.M.

(2024) Nature 628: 442-449

  • DOI: https://doi.org/10.1038/s41586-024-07250-1
  • Primary Citation of Related Structures:  
    8TL6

  • PubMed Abstract: 

    Whereas oncogenes can potentially be inhibited with small molecules, the loss of tumour suppressors is more common and is problematic because the tumour-suppressor proteins are no longer present to be targeted. Notable examples include SMARCB1-mutant cancers, which are highly lethal malignancies driven by the inactivation of a subunit of SWI/SNF (also known as BAF) chromatin-remodelling complexes. Here, to generate mechanistic insights into the consequences of SMARCB1 mutation and to identify vulnerabilities, we contributed 14 SMARCB1-mutant cell lines to a near genome-wide CRISPR screen as part of the Cancer Dependency Map Project 1-3 . We report that the little-studied gene DDB1-CUL4-associated factor 5 (DCAF5) is required for the survival of SMARCB1-mutant cancers. We show that DCAF5 has a quality-control function for SWI/SNF complexes and promotes the degradation of incompletely assembled SWI/SNF complexes in the absence of SMARCB1. After depletion of DCAF5, SMARCB1-deficient SWI/SNF complexes reaccumulate, bind to target loci and restore SWI/SNF-mediated gene expression to levels that are sufficient to reverse the cancer state, including in vivo. Consequently, cancer results not from the loss of SMARCB1 function per se, but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of ubiquitin-mediated quality-control factors may effectively reverse the malignant state of some cancers driven by disruption of tumour suppressor complexes.


  • Organizational Affiliation

    Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1864Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 5986Homo sapiensMutation(s): 0 
Gene Names: DCAF5BCRG2KIAA1824WDR22
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JK2 (Homo sapiens)
Explore Q96JK2 
Go to UniProtKB:  Q96JK2
PHAROS:  Q96JK2
GTEx:  ENSG00000139990 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JK2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1C [auth E]126Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
GTEx:  ENSG00000130311 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BW61
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.1.2
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Mark FoundationUnited States6331505

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references