6WQU | pdb_00006wqu

CSL (RBPJ) bound to Notch3 RAM and DNA

• PDB DOI: https://doi.org/10.2210/pdb6WQU/pdb
• NAKB: 6WQU

• Classification: TRANSCRIPTION/SIGNALING PROTEIN/DNA
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-29 Released: 2021-03-31 
• Deposition Author(s): Kovall, R.A., Gagliani, E., Hall, D.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.233 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

PIM-induced phosphorylation of Notch3 promotes breast cancer tumorigenicity in a CSL-independent fashion.

Landor, S.K.J., Santio, N.M., Eccleshall, W.B., Paramonov, V.M., Gagliani, E.K., Hall, D., Jin, S.B., Dahlstrom, K.M., Salminen, T.A., Rivero-Muller, A., Lendahl, U., Kovall, R.A., Koskinen, P.J., Sahlgren, C.

(2021) J Biological Chem 296: 100593-100593

• PubMed: 33775697 
• DOI: https://doi.org/10.1016/j.jbc.2021.100593
• Primary Citation Related Structures: 
  6WQU


• PubMed Abstract: 
  

  Dysregulation of the developmentally important Notch signaling pathway is implicated in several types of cancer, including breast cancer. However, the specific roles and regulation of the four different Notch receptors have remained elusive. We have previously reported that the oncogenic PIM kinases phosphorylate Notch1 and Notch3. Phosphorylation of Notch1 within the second nuclear localization sequence of its intracellular domain (ICD) enhances its transcriptional activity and tumorigenicity. In this study, we analyzed Notch3 phosphorylation and its functional impact. Unexpectedly, we observed that the PIM target sites are not conserved between Notch1 and Notch3. Notch3 ICD (N3ICD) is phosphorylated within a domain, which is essential for formation of a transcriptionally active complex with the DNA-binding protein CSL. Through molecular modeling, X-ray crystallography, and isothermal titration calorimetry, we demonstrate that phosphorylation of N3ICD sterically hinders its interaction with CSL and thereby inhibits its CSL-dependent transcriptional activity. Surprisingly however, phosphorylated N3ICD still maintains tumorigenic potential in breast cancer cells under estrogenic conditions, which support PIM expression. Taken together, our data indicate that PIM kinases modulate the signaling output of different Notch paralogs by targeting distinct protein domains and thereby promote breast cancer tumorigenesis via both CSL-dependent and CSL-independent mechanisms.

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Organizational Affiliation: 
• Faculty of Science and Engineering/Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland.
Department of Biology, University of Turku, Turku, Finland.
Faculty of Science and Engineering/Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland; Department of Biology, University of Turku, Turku, Finland.
Faculty of Science and Engineering/Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland; Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland.
Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Ohio, USA.
Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.
Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi, Turku, Finland.
Faculty of Science and Engineering/Cell Biology, Åbo Akademi University, Turku, Finland; Department of Biology, University of Turku, Turku, Finland.
Department of Biology, University of Turku, Turku, Finland. Electronic address: [e-mail].
Faculty of Science and Engineering/Cell Biology, Åbo Akademi University, Turku, Finland; Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 59.36 kDa 
• Atom Count: 4,131 
• Modeled Residue Count: 462 
• Deposited Residue Count: 471 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombining binding protein suppressor of hairless	C	423	Mus musculus	Mutation(s): 0  Gene Names: Rbpj, Igkjrb1, Igkrsbp, Rbpsuh
UniProt & NIH Common Fund Data Resources
Find proteins for P31266 (Mus musculus) Explore P31266  Go to UniProtKB:  P31266
IMPC:  MGI:96522

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurogenic locus notch homolog protein 3	D	18	Homo sapiens	Mutation(s): 0  Gene Names: NOTCH3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM47 (Homo sapiens) Explore Q9UM47  Go to UniProtKB:  Q9UM47
PHAROS:  Q9UM47 GTEx:  ENSG00000074181

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*GP*GP*T)-3')	A	15	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*AP*CP*CP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3')	B	15	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.233 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.45	α = 90
b = 97.66	β = 90
c = 104.62	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Kovall, R.A., Gagliani, E., Hall, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA178974

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2021-07-14
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description