6Q0R

Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ...

    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.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. eric_fischer@dfci.harvard.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. eric_fischer@dfci.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
864Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DDB1- and CUL4-associated factor 15
B
276Homo sapiensMutation(s): 0 
Gene Names: DCAF15 (C19orf72)
Find proteins for Q66K64 (Homo sapiens)
Go to Gene View: DCAF15
Go to UniProtKB:  Q66K64
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DDB1- and CUL4-associated factor 15
C
263Homo sapiensMutation(s): 0 
Gene Names: DCAF15 (C19orf72)
Find proteins for Q66K64 (Homo sapiens)
Go to Gene View: DCAF15
Go to UniProtKB:  Q66K64
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 39
D
107Homo sapiensMutation(s): 0 
Gene Names: RBM39 (HCC1, RNPC2)
Find proteins for Q14498 (Homo sapiens)
Go to Gene View: RBM39
Go to UniProtKB:  Q14498
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DET1- and DDB1-associated protein 1
E
126Homo sapiensMutation(s): 0 
Gene Names: DDA1 (C19orf58, PCIA1)
Find proteins for Q9BW61 (Homo sapiens)
Go to Gene View: DDA1
Go to UniProtKB:  Q9BW61
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
OXM
Query on OXM

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Download CCD File 
B
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
 Ligand Interaction
O6M
Query on O6M

Download SDF File 
Download CCD File 
B
3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide
C17 H12 N4 O2 S
LWGUASZLXHYWIV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.108α = 90.00
b = 93.600β = 90.00
c = 258.439γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence
  • Version 1.3: 2020-01-01
    Type: Database references