8DFP image
Entry Detail
PDB ID:
8DFP
EMDB ID:
Keywords:
Title:
Ectodomain of full-length KIT(DupA502,Y503)-SCF dimers
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-06-22
Release Date:
2023-03-29
Method Details:
Experimental Method:
Resolution:
3.17 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Isoform 2 of Mast/stem cell growth factor receptor Kit
Mutations:K619A
Chain IDs:A, B
Chain Length:982
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Soluble KIT ligand
Chain IDs:C, D
Chain Length:128
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention.
Proc.Natl.Acad.Sci.USA 120 e2300054120 e2300054120 (2023)
PMID: 36943885 DOI: 10.1073/pnas.2300054120

Abstact

The receptor tyrosine kinase KIT and its ligand stem cell factor (SCF) are required for the development of hematopoietic stem cells, germ cells, and other cells. A variety of human cancers, such as acute myeloid leukemia, gastrointestinal stromal tumor, and mast cell leukemia, are driven by somatic gain-of-function KIT mutations. Here, we report cryo electron microscopy (cryo-EM) structural analyses of full-length wild-type and two oncogenic KIT mutants, which show that the overall symmetric arrangement of the extracellular domain of ligand-occupied KIT dimers contains asymmetric D5 homotypic contacts juxtaposing the plasma membrane. Mutational analysis of KIT reveals in D5 region an "Achilles heel" for therapeutic intervention. A ligand-sensitized oncogenic KIT mutant exhibits a more comprehensive and stable D5 asymmetric conformation. A constitutively active ligand-independent oncogenic KIT mutant adopts a V-shaped conformation solely held by D5-mediated contacts. Binding of SCF to this mutant fully restores the conformation of wild-type KIT dimers, including the formation of salt bridges responsible for D4 homotypic contacts and other hallmarks of SCF-induced KIT dimerization. These experiments reveal an unexpected structural plasticity of oncogenic KIT mutants and a therapeutic target in D5.

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Primary Citation of related structures