2E9W

Crystal structure of the extracellular domain of Kit in complex with stem cell factor (SCF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Activation of the Receptor Tyrosine Kinase KIT by Stem Cell Factor

Yuzawa, S.Opatowsky, Y.Zhang, Z.Mandiyan, V.Lax, I.Schlessinger, J.

(2007) Cell 130: 323-334

  • DOI: 10.1016/j.cell.2007.05.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Stem Cell Factor (SCF) initiates its multiple cellular responses by binding to the ectodomain of KIT, resulting in tyrosine kinase activation. We describe the crystal structure of the entire ectodomain of KIT before and after SCF stimulation. The str ...

    Stem Cell Factor (SCF) initiates its multiple cellular responses by binding to the ectodomain of KIT, resulting in tyrosine kinase activation. We describe the crystal structure of the entire ectodomain of KIT before and after SCF stimulation. The structures show that KIT dimerization is driven by SCF binding whose sole role is to bring two KIT molecules together. Receptor dimerization is followed by conformational changes that enable lateral interactions between membrane proximal Ig-like domains D4 and D5 of two KIT molecules. Experiments with cultured cells show that KIT activation is compromised by point mutations in amino acids critical for D4-D4 interaction. Moreover, a variety of oncogenic mutations are mapped to the D5-D5 interface. Since key hallmarks of KIT structures, ligand-induced receptor dimerization, and the critical residues in the D4-D4 interface, are conserved in other receptors, the mechanism of KIT stimulation unveiled in this report may apply for other receptor activation.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor
A, B
489Homo sapiensMutation(s): 2 
Gene Names: KIT (SCFR)
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Go to Gene View: KIT
Go to UniProtKB:  P10721
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Kit ligand
C, D
141Homo sapiensMutation(s): 0 
Gene Names: KITLG (MGF, SCF)
Find proteins for P21583 (Homo sapiens)
Go to Gene View: KITLG
Go to UniProtKB:  P21583
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 269.477α = 90.00
b = 52.072β = 108.00
c = 189.791γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance