2O26

Structure of a class III RTK signaling assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases.

Liu, H.Chen, X.Focia, P.J.He, X.

(2007) Embo J. 26: 891-901

  • DOI: 10.1038/sj.emboj.7601545
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Stem cell factor (SCF) binds to and activates the KIT receptor, a class III receptor tyrosine kinase (RTK), to stimulate diverse processes including melanogenesis, gametogenesis and hematopoeisis. Dysregulation of KIT activation is associated with ma ...

    Stem cell factor (SCF) binds to and activates the KIT receptor, a class III receptor tyrosine kinase (RTK), to stimulate diverse processes including melanogenesis, gametogenesis and hematopoeisis. Dysregulation of KIT activation is associated with many cancers. We report a 2.5 A crystal structure of the functional core of SCF bound to the extracellular ligand-binding domains of KIT. The structure reveals a 'wrapping' SCF-recognition mode by KIT, in which KIT adopts a bent conformation to facilitate each of its first three immunoglobulin (Ig)-like domains to interact with SCF. Three surface epitopes on SCF, an extended loop, the B and C helices, and the N-terminal segment, contact distinct KIT domains, with two of the epitopes undergoing large conformational changes upon receptor binding. The SCF/KIT complex reveals a unique RTK dimerization assembly, and a novel recognition mode between four-helix bundle cytokines and Ig-family receptors. It serves as a framework for understanding the activation mechanisms of class III RTKs.


    Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kit ligand
A, B, E, F
145Mus musculusMutation(s): 0 
Gene Names: Kitlg (Kitl, Mgf, Sl, Slf)
Find proteins for P20826 (Mus musculus)
Go to UniProtKB:  P20826
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor
X, Y, U, W
290Mus musculusMutation(s): 1 
Gene Names: Kit (Sl)
EC: 2.7.10.1
Find proteins for P05532 (Mus musculus)
Go to UniProtKB:  P05532
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
U, W, X, Y
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
W
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
U, W, X, Y
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
U, W, X, Y
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.849α = 90.00
b = 200.154β = 91.42
c = 82.023γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance