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 1.3 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: 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 ...

    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 Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. eric_fischer@dfci.harvard.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1A864Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Find proteins for Q16531 (Homo sapiens)
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Go to UniProtKB:  Q16531
PHAROS:  Q16531
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UniProt GroupQ16531
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15B276Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
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PHAROS:  Q66K64
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15C263Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 39D107Homo sapiensMutation(s): 0 
Gene Names: RBM39HCC1RNPC2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1E126Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
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Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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