3FL7

Crystal structure of the human ephrin A2 ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Architecture of Eph receptor clusters.

Himanen, J.P.Yermekbayeva, L.Janes, P.W.Walker, J.R.Xu, K.Atapattu, L.Rajashankar, K.R.Mensinga, A.Lackmann, M.Nikolov, D.B.Dhe-Paganon, S.

(2010) Proc Natl Acad Sci U S A 107: 10860-10865

  • DOI: 10.1073/pnas.1004148107
  • Structures With Same Primary Citation

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

    Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanism underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.


    Related Citations: 
    • Recruitment of Eph receptors into signaling clusters does not require ephrin contact.
      Wimmer-Kleikamp, S.H., Janes, P.W., Squire, A., Bastiaens, P.I., Lackmann, M.
      (2004) J Cell Biol 164: 661
    • Distinct subdomains of the EphA3 receptor mediate ligand binding and receptor dimerization.
      Lackmann, M., Oates, A.C., Dottori, M., Smith, F.M., Do, C., Power, M., Kravets, L., Boyd, A.W.
      (1998) J Biol Chem 273: 20228
    • 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

    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin receptor
A
536Homo sapiensMutation(s): 0 
Gene Names: ECKEPHA2hCG_24712RP11-276H7.1-001
EC: 2.7.10.1
Find proteins for P29317 (Homo sapiens)
Go to UniProtKB:  P29317
NIH Common Fund Data Resources
PHAROS  P29317
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.358α = 90
b = 89.992β = 90
c = 136.476γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance