6SJ7

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 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

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex.

Bussiere, D.E.Xie, L.Srinivas, H.Shu, W.Burke, A.Be, C.Zhao, J.Godbole, A.King, D.Karki, R.G.Hornak, V.Xu, F.Cobb, J.Carte, N.Frank, A.O.Frommlet, A.Graff, P.Knapp, M.Fazal, A.Okram, B.Jiang, S.Michellys, P.Y.Beckwith, R.Voshol, H.Wiesmann, C.Solomon, J.M.Paulk, J.

(2020) Nat Chem Biol 16: 15-23

  • DOI: 10.1038/s41589-019-0411-6
  • Primary Citation of Related Structures:  
    6SJ7, 6UD7, 6UE5

  • PubMed Abstract: 
  • The anticancer agent indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor, leading to RBM39 ubiquitination and proteasome-mediated degradation ...

    The anticancer agent indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor, leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which indisulam mediates the DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-indisulam-RBM39(RRM2) complex structure to a resolution of 2.3 Å. DCAF15 has a distinct topology that embraces the RBM39(RRM2) domain largely via non-polar interactions, and indisulam binds between DCAF15 and RBM39(RRM2), coordinating additional interactions between the two proteins. Studies with RBM39 point mutants and indisulam analogs validated the structural model and defined the RBM39 α-helical degron motif. The degron is found only in RBM23 and RBM39, and only these proteins were detectably downregulated in indisulam-treated HCT116 cells. This work further explains how indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade additional targets.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research, Cambridge, MA, USA. josh.paulk@novartis.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15A601Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
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Find proteins for Q66K64 (Homo sapiens)
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Go to UniProtKB:  Q66K64
PHAROS:  Q66K64
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UniProt GroupQ66K64
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1B1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
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Find proteins for Q16531 (Homo sapiens)
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PHAROS:  Q16531
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UniProt GroupQ16531
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA binding protein 39C81Homo sapiensMutation(s): 0 
Gene Names: DKFZp781I1140RBM39HCC1RNPC2
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Find proteins for Q14498 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1D101Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
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Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
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UniProt GroupQ9BW61
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EF6 (Subject of Investigation/LOI)
Query on EF6

Download Ideal Coordinates CCD File 
E [auth A]N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide
C14 H12 Cl N3 O4 S2
SETFNECMODOHTO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2019-12-18 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references