6Q0V

Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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This is version 1.4 of the entry. See complete history


Literature

Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15.

Faust, T.B.Yoon, H.Nowak, R.P.Donovan, K.A.Li, Z.Cai, Q.Eleuteri, N.A.Zhang, T.Gray, N.S.Fischer, E.S.

(2020) Nat Chem Biol 16: 7-14

  • DOI: https://doi.org/10.1038/s41589-019-0378-3
  • Primary Citation of Related Structures:  
    6Q0R, 6Q0V, 6Q0W

  • PubMed Abstract: 

    The investigational drugs E7820, indisulam and tasisulam (aryl-sulfonamides) promote the degradation of the splicing factor RBM39 in a proteasome-dependent mechanism. While the activity critically depends on the cullin RING ligase substrate receptor DCAF15, the molecular details remain elusive. Here we present the cryo-EM structure of the DDB1-DCAF15-DDA1 core ligase complex bound to RBM39 and E7820 at a resolution of 4.4 Å, together with crystal structures of engineered subcomplexes. We show that DCAF15 adopts a new fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigate low affinity interactions between aryl-sulfonamides and DCAF15. Our data demonstrate how aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high-affinity ligand, which has broad implications for the de novo discovery of molecular glue degraders.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.


Macromolecules
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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
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15276Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
UniProt & NIH Common Fund Data Resources
Find proteins for Q66K64 (Homo sapiens)
Explore Q66K64 
Go to UniProtKB:  Q66K64
PHAROS:  Q66K64
GTEx:  ENSG00000132017 
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UniProt GroupQ66K64
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15263Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
UniProt & NIH Common Fund Data Resources
Find proteins for Q66K64 (Homo sapiens)
Explore Q66K64 
Go to UniProtKB:  Q66K64
PHAROS:  Q66K64
GTEx:  ENSG00000132017 
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UniProt GroupQ66K64
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 39107Homo sapiensMutation(s): 0 
Gene Names: RBM39HCC1RNPC2
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Find proteins for Q14498 (Homo sapiens)
Explore Q14498 
Go to UniProtKB:  Q14498
PHAROS:  Q14498
GTEx:  ENSG00000131051 
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UniProt GroupQ14498
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1126Homo 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 
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P7M (Subject of Investigation/LOI)
Query on P7M

Download Ideal Coordinates CCD File 
F [auth B]N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide
C11 H6 Br Cl2 N O3 S2
WWONFUQGBVOKOF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.769α = 90
b = 94.613β = 90
c = 260.39γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214608
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1F32CA232772-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description