2O27 | pdb_00002o27

Structure of a class III RTK signaling assembly


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.266 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2O27

This is version 1.4 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: https://doi.org/10.1038/sj.emboj.7601545
  • Primary Citation Related Structures: 
    2O26, 2O27

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 32.89 kDa 
  • Atom Count: 2,467 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 290 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kit ligand
A, B
145Mus musculusMutation(s): 0 
Gene Names: KitlgKitlMgfSlSlf
UniProt
Find proteins for P20826 (Mus musculus)
Explore P20826 
Go to UniProtKB:  P20826
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20826
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.266 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.27α = 90
b = 43.27β = 90
c = 248.433γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary