1KGY

Crystal Structure of the EphB2-ephrinB2 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of an Eph receptor-ephrin complex.

Himanen, J.P., Rajashankar, K.R., Lackmann, M., Cowan, C.A., Henkemeyer, M., Nikolov, D.B.

(2001) Nature 414: 933-938

  • DOI: 10.1038/414933a
  • Also Cited By: 3GXU, 3FL7

  • PubMed Abstract: 

    • The Eph family of receptor tyrosine kinases and their membrane-anchored ephrin ligands are important in regulating cell-cell interactions as they initiate a unique bidirectional signal transduction cascade whereby information is communicated into bot ...

    The Eph family of receptor tyrosine kinases and their membrane-anchored ephrin ligands are important in regulating cell-cell interactions as they initiate a unique bidirectional signal transduction cascade whereby information is communicated into both the Eph-expressing and the ephrin-expressing cells. Initially identified as regulators of axon pathfinding and neuronal cell migration, Ephs and ephrins are now known to have roles in many other cell-cell interactions, including those of vascular endothelial cells and specialized epithelia. Here we report the crystal structure of the complex formed between EphB2 and ephrin-B2, determined at 2.7 A resolution. Each Eph receptor binds an ephrin ligand through an expansive dimerization interface dominated by the insertion of an extended ephrin loop into a channel at the surface of the receptor. Two Eph-Ephrin dimers then join to form a tetramer, in which each ligand interacts with two receptors and each receptor interacts with two ligands. The Eph and ephrin molecules are precisely positioned and orientated in these complexes, promoting higher-order clustering and the initiation of bidirectional signalling.

    Organizational Affiliation: 

    Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-B RECEPTOR 2
A, B, C, D
181Mus musculusGene Names: Ephb2 (Epth3, Nuk, Sek3)
EC: 2.7.10.1
Find proteins for P54763 (Mus musculus)
Go to UniProtKB:  P54763
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EPHRIN-B2
E, F, G, H
138Mus musculusGene Names: Efnb2 (Elf2, Epl5, Eplg5, Htkl, Lerk5)
Find proteins for P52800 (Mus musculus)
Go to UniProtKB:  P52800
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.000α = 69.00
b = 78.000β = 75.00
c = 78.000γ = 69.00
Software Package:
Software NamePurpose
CNSrefinement
MARdata collection
SCALEPACKdata scaling
MARdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-08
    Type: Structure summary