6PY8

Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Extension of the Notch intracellular domain ankyrin repeat stack by NRARP promotes feedback inhibition of Notch signaling.

Jarrett, S.M.Seegar, T.C.M.Andrews, M.Adelmant, G.Marto, J.A.Aster, J.C.Blacklow, S.C.

(2019) Sci Signal 12

  • DOI: 10.1126/scisignal.aay2369
  • Primary Citation of Related Structures:  
    6PY8

  • PubMed Abstract: 
  • Canonical Notch signaling relies on regulated proteolysis of the receptor Notch to generate a nuclear effector that induces the transcription of Notch-responsive genes. In higher organisms, one Notch-responsive gene that is activated in many different cell types encodes the Notch-regulated ankyrin repeat protein (NRARP), which acts as a negative feedback regulator of Notch responses ...

    Canonical Notch signaling relies on regulated proteolysis of the receptor Notch to generate a nuclear effector that induces the transcription of Notch-responsive genes. In higher organisms, one Notch-responsive gene that is activated in many different cell types encodes the Notch-regulated ankyrin repeat protein (NRARP), which acts as a negative feedback regulator of Notch responses. Here, we showed that NRARP inhibited the growth of Notch-dependent T cell acute lymphoblastic leukemia (T-ALL) cell lines and bound directly to the core Notch transcriptional activation complex (NTC), requiring both the transcription factor RBPJ and the Notch intracellular domain (NICD), but not Mastermind-like proteins or DNA. The crystal structure of an NRARP-NICD1-RBPJ-DNA complex, determined to 3.75 Å resolution, revealed that the assembly of NRARP-NICD1-RBPJ complexes relied on simultaneous engagement of RBPJ and NICD1, with the three ankyrin repeats of NRARP extending the Notch1 ankyrin repeat stack. Mutations at the NRARP-NICD1 interface disrupted entry of the proteins into NTCs and abrogated feedback inhibition in Notch signaling assays in cultured cells. Forced expression of NRARP reduced the abundance of NICD in cells, suggesting that NRARP may promote the degradation of NICD. These studies establish the structural basis for NTC engagement by NRARP and provide insights into a critical negative feedback mechanism that regulates Notch signaling.


    Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Notch-regulated ankyrin repeat-containing proteinA [auth B],
B [auth G]
114Homo sapiensMutation(s): 0 
Gene Names: NRARP
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z6K4 (Homo sapiens)
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PHAROS:  Q7Z6K4
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UniProt GroupQ7Z6K4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Recombining binding protein suppressor of hairlessG [auth C],
H [auth E]
444Homo sapiensMutation(s): 0 
Gene Names: RBPJIGKJRBIGKJRB1RBPJKRBPSUH
UniProt & NIH Common Fund Data Resources
Find proteins for Q06330 (Homo sapiens)
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UniProt GroupQ06330
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Neurogenic locus notch homolog protein 1I [auth F],
J [auth K]
369Homo sapiensMutation(s): 0 
Gene Names: NOTCH1TAN1
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens)
Explore P46531 
Go to UniProtKB:  P46531
PHAROS:  P46531
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UniProt GroupP46531
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNAC [auth A],
D [auth X]
16Homo sapiens
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNAE [auth D],
F [auth Y]
16Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.270 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.88α = 90
b = 103.65β = 90
c = 301.42γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata processing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35 CA220340

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 2.0: 2019-09-04
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Structure summary
  • Version 2.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 2.2: 2020-02-26
    Changes: Database references