6M8Q

Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma.

Ross, N.T.Lohmann, F.Carbonneau, S.Fazal, A.Weihofen, W.A.Gleim, S.Salcius, M.Sigoillot, F.Henault, M.Carl, S.H.Rodriguez-Molina, J.B.Miller, H.R.Brittain, S.M.Murphy, J.Zambrowski, M.Boynton, G.Wang, Y.Chen, A.Molind, G.J.Wilbertz, J.H.Artus-Revel, C.G.Jia, M.Akinjiyan, F.A.Turner, J.Knehr, J.Carbone, W.Schuierer, S.Reece-Hoyes, J.S.Xie, K.Saran, C.Williams, E.T.Roma, G.Spencer, M.Jenkins, J.George, E.L.Thomas, J.R.Michaud, G.Schirle, M.Tallarico, J.Passmore, L.A.Chao, J.A.Beckwith, R.E.J.

(2020) Nat Chem Biol 16: 50-59

  • DOI: 10.1038/s41589-019-0424-1
  • Primary Citation of Related Structures:  
    6M8Q

  • PubMed Abstract: 
  • The post-genomic era has seen many advances in our understanding of cancer pathways, yet resistance and tumor heterogeneity necessitate multiple approaches to target even monogenic tumors. Here, we combine phenotypic screening with chemical genetics to identify pre-messenger RNA endonuclease cleavage and polyadenylation specificity factor 3 (CPSF3) as the target of JTE-607, a small molecule with previously unknown target ...

    The post-genomic era has seen many advances in our understanding of cancer pathways, yet resistance and tumor heterogeneity necessitate multiple approaches to target even monogenic tumors. Here, we combine phenotypic screening with chemical genetics to identify pre-messenger RNA endonuclease cleavage and polyadenylation specificity factor 3 (CPSF3) as the target of JTE-607, a small molecule with previously unknown target. We show that CPSF3 represents a synthetic lethal node in a subset of acute myeloid leukemia (AML) and Ewing's sarcoma cancer cell lines. Inhibition of CPSF3 by JTE-607 alters expression of known downstream effectors in AML and Ewing's sarcoma lines, upregulates apoptosis and causes tumor-selective stasis in mouse xenografts. Mechanistically, it prevents the release of newly synthesized pre-mRNAs, resulting in read-through transcription and the formation of DNA-RNA hybrid R-loop structures. This study implicates pre-mRNA processing, and specifically CPSF3, as a druggable target providing an avenue to therapeutic intervention in cancer.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Cambridge, MA, USA. rohan.beckwith@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 3A, B478Homo sapiensMutation(s): 0 
Gene Names: CPSF3CPSF73
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKF6 (Homo sapiens)
Explore Q9UKF6 
Go to UniProtKB:  Q9UKF6
PHAROS:  Q9UKF6
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.222α = 90
b = 106.222β = 90
c = 206.035γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references