6M8Q | pdb_00006m8q

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6M8Q

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/s41589-019-0424-1
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 110.23 kDa 
  • Atom Count: 7,824 
  • Modeled Residue Count: 904 
  • Deposited Residue Count: 956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 3
A, B
478Homo 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
GTEx:  ENSG00000119203 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKF6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JBG
(Subject of Investigation/LOI)

Query on JBG



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine
C23 H27 Cl2 N3 O5
XEBIFCYTYHBFTB-SFHVURJKSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
K [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
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

View Full Validation Report



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
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description