4M4P

Crystal structure of EPHA4 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.081 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Insights into Eph receptor tyrosine kinase activation from crystal structures of the EphA4 ectodomain and its complex with ephrin-A5.

Xu, K.Tzvetkova-Robev, D.Xu, Y.Goldgur, Y.Chan, Y.P.Himanen, J.P.Nikolov, D.B.

(2013) Proc.Natl.Acad.Sci.USA 110: 14634-14639

  • DOI: 10.1073/pnas.1311000110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eph receptor tyrosine kinases and their ephrin ligands mediate cell signaling during normal and oncogenic development. Eph signaling is initiated in a multistep process leading to the assembly of higher-order Eph/ephrin clusters that set off bidirect ...

    Eph receptor tyrosine kinases and their ephrin ligands mediate cell signaling during normal and oncogenic development. Eph signaling is initiated in a multistep process leading to the assembly of higher-order Eph/ephrin clusters that set off bidirectional signaling in interacting cells. Eph and ephrins are divided in two subclasses based on their abilities to bind and activate each other and on sequence conservation. EphA4 is an exception to the general rule because it can be activated by both A- and B-class ephrin ligands. Here we present high-resolution structures of the complete EphA4 ectodomain and its complexes with ephrin-A5. The structures reveal how ligand binding promotes conformational changes in the EphA4 ligand-binding domain allowing the formation of signaling clusters at the sites of cell-cell contact. In addition, the structural data, combined with structure-based mutagenesis, reveal a previously undescribed receptor-receptor interaction between the EphA4 ligand-binding and membrane-proximal fibronectin domains, which is functionally important for efficient receptor activation.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 4
A
518Homo sapiensMutation(s): 0 
Gene Names: EPHA4 (HEK8, SEK, TYRO1)
EC: 2.7.10.1
Find proteins for P54764 (Homo sapiens)
Go to Gene View: EPHA4
Go to UniProtKB:  P54764
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.081 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 112.589α = 90.00
b = 112.589β = 90.00
c = 49.552γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
ADSCdata collection
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release