4PGZ

Structural basis of KIT activation by oncogenic mutations in the extracellular region reveals a zipper-like mechanism for ligand-dependent or oncogenic receptor tyrosine kinase activation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The strength and cooperativity of KIT ectodomain contacts determine normal ligand-dependent stimulation or oncogenic activation in cancer.

Reshetnyak, A.V.Opatowsky, Y.Boggon, T.J.Folta-Stogniew, E.Tome, F.Lax, I.Schlessinger, J.

(2015) Mol Cell 57: 191-201

  • DOI: https://doi.org/10.1016/j.molcel.2014.11.021
  • Primary Citation of Related Structures:  
    4PGZ

  • PubMed Abstract: 

    The receptor tyrosine kinase KIT plays an important role in development of germ cells, hematopoietic cells, and interstitial pacemaker cells. Oncogenic KIT mutations play an important "driver" role in gastrointestinal stromal tumors, acute myeloid leukemias, and melanoma, among other cancers. Here we describe the crystal structure of a recurring somatic oncogenic mutation located in the C-terminal Ig-like domain (D5) of the ectodomain, rendering KIT tyrosine kinase activity constitutively activated. The structural analysis, together with biochemical and biophysical experiments and detailed analyses of the activities of a variety of oncogenic KIT mutations, reveals that the strength of homotypic contacts and the cooperativity in the action of D4D5 regions determines whether KIT is normally regulated or constitutively activated in cancers. We propose that cooperative interactions mediated by multiple weak homotypic contacts between receptor molecules are responsible for regulating normal ligand-dependent or oncogenic RTK activation via a "zipper-like" mechanism for receptor activation.


  • Organizational Affiliation

    The Biophysical Resource, Yale University School of Medicine, New Haven, CT 06520, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor KitA [auth C],
B [auth A],
C [auth B]
208Homo sapiensMutation(s): 0 
Gene Names: KITSCFR
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens)
Explore P10721 
Go to UniProtKB:  P10721
GTEx:  ENSG00000157404 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.592α = 90
b = 63.548β = 117.46
c = 81.547γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KolltanUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Structure summary