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 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1073/pnas.1004148107
  • Primary Citation of Related Structures:  
    3C8X, 3CZU, 3FL7, 3MBW, 3MX0

  • 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 bidirectional signaling in interacting cells ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ephrin receptor536Homo sapiensMutation(s): 0 
Gene Names: ECKEPHA2hCG_24712RP11-276H7.1-001
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens)
Explore P29317 
Go to UniProtKB:  P29317
PHAROS:  P29317
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth 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

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary