5NJJ

PTB domain of human Numb isoform-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Numb-Mdm2 fuzzy complex reveals an isoform-specific involvement of Numb in breast cancer.

Colaluca, I.N.Basile, A.Freiburger, L.D'Uva, V.Disalvatore, D.Vecchi, M.Confalonieri, S.Tosoni, D.Cecatiello, V.Malabarba, M.G.Yang, C.J.Kainosho, M.Sattler, M.Mapelli, M.Pece, S.Di Fiore, P.P.

(2018) J Cell Biol 217: 745-762

  • DOI: https://doi.org/10.1083/jcb.201709092
  • Primary Citation of Related Structures:  
    5NJJ, 5NJK

  • PubMed Abstract: 

    Numb functions as an oncosuppressor by inhibiting Notch signaling and stabilizing p53. This latter effect depends on the interaction of Numb with Mdm2, the E3 ligase that ubiquitinates p53 and commits it to degradation. In breast cancer (BC), loss of Numb results in a reduction of p53-mediated responses including sensitivity to genotoxic drugs and maintenance of homeostasis in the stem cell compartment. In this study, we show that the Numb-Mdm2 interaction represents a fuzzy complex mediated by a short Numb sequence encompassing its alternatively spliced exon 3 (Ex3), which is necessary and sufficient to inhibit Mdm2 and prevent p53 degradation. Alterations in the Numb splicing pattern are critical in BC as shown by increased chemoresistance of tumors displaying reduced levels of Ex3-containing isoforms, an effect that could be mechanistically linked to diminished p53 levels. A reduced level of Ex3-less Numb isoforms independently predicts poor outcome in BCs harboring wild-type p53. Thus, we have uncovered an important mechanism of chemoresistance and progression in p53-competent BCs.


  • Organizational Affiliation

    The FIRC Institute for Molecular Oncology Foundation, Milan, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein numb homolog
A, B, C, D
156Homo sapiensMutation(s): 0 
Gene Names: NUMB
UniProt & NIH Common Fund Data Resources
Find proteins for P49757 (Homo sapiens)
Explore P49757 
Go to UniProtKB:  P49757
PHAROS:  P49757
GTEx:  ENSG00000133961 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49757
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-TYR-ILE-GLY-PRO-PTR-LEU
E, F, G, H
7Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
E, F, G, H
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.77α = 90
b = 120.44β = 90
c = 237.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG18629, IG14404, IG11904

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary