1NUK

CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE EPHB2 RECEPTOR TYROSINE KINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2.

Himanen, J.P.Henkemeyer, M.Nikolov, D.B.

(1998) Nature 396: 486-491

  • DOI: 10.1038/24904

  • PubMed Abstract: 
  • The Eph receptors, which bind a group of cell-membrane-anchored ligands known as ephrins, represent the largest subfamily of receptor tyrosine kinases (RTKs). They are predominantly expressed in the developing and adult nervous system and are importa ...

    The Eph receptors, which bind a group of cell-membrane-anchored ligands known as ephrins, represent the largest subfamily of receptor tyrosine kinases (RTKs). They are predominantly expressed in the developing and adult nervous system and are important in contact-mediated axon guidance, axon fasciculation and cell migration. Eph receptors are unique among other RTKs in that they fall into two subclasses with distinct ligand specificities, and in that they can themselves function as ligands to activate bidirectional cell-cell signalling. We report here the crystal structure at 2.9 A resolution of the amino-terminal ligand-binding domain of the EphB2 receptor (also known as Nuk). The domain folds into a compact jellyroll beta-sandwich composed of 11 antiparallel beta-strands. Using structure-based mutagenesis, we have identified an extended loop that is important for ligand binding and class specificity. This loop, which is conserved within but not between Eph RTK subclasses, packs against the concave beta-sandwich surface near positions at which missense mutations cause signalling defects, localizing the ligand-binding region on the surface of the receptor.


    Organizational Affiliation

    Cellular Biochemistry and Biophysics Program, Memorial-Sloan-Kettering Cancer Center, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TYROSINE-PROTEIN KINASE RECEPTOR EPH)
A
183Mus musculusGene Names: Ephb2 (Epth3, Nuk, Sek3)
EC: 2.7.10.1
Find proteins for P54763 (Mus musculus)
Go to UniProtKB:  P54763
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 55.150α = 90.00
b = 55.150β = 90.00
c = 158.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance