4BKF

crystal structure of the human EphA4 ectodomain in complex with human ephrinB3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.65 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.327 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses

Seiradake, E.Schaupp, A.Del Toro Ruiz, D.Kaufmann, R.Mitakidis, N.Harlos, K.Aricescu, A.R.Klein, R.Jones, E.Y.

(2013) Nat.Struct.Mol.Biol. 20: 958

  • DOI: 10.1038/nsmb.2617
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Functional outcomes of ephrin binding to Eph receptors (Ephs) range from cell repulsion to adhesion. Here we used cell collapse and stripe assays, showing contrasting effects of human ephrinA5 binding to EphA2 and EphA4. Despite equivalent ligand bin ...

    Functional outcomes of ephrin binding to Eph receptors (Ephs) range from cell repulsion to adhesion. Here we used cell collapse and stripe assays, showing contrasting effects of human ephrinA5 binding to EphA2 and EphA4. Despite equivalent ligand binding affinities, EphA4 triggered greater cell collapse, whereas EphA2-expressing cells adhered better to ephrinA5-coated surfaces. Chimeric receptors showed that the ectodomain is a major determinant of cell response. We report crystal structures of EphA4 ectodomain alone and in complexes with ephrinB3 and ephrinA5. These revealed closed clusters with a dimeric or circular arrangement in the crystal lattice, contrasting with extended arrays previously observed for EphA2 ectodomain. Localization microscopy showed that ligand-stimulated EphA4 induces smaller clusters than does EphA2. Mutant Ephs link these characteristics to interactions observed in the crystal lattices, suggesting a mechanism by which distinctive ectodomain surfaces determine clustering, and thereby signaling, properties.


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-A RECEPTOR 4
A, B
568Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EPHRIN-B3
C, D
183Homo sapiensMutation(s): 0 
Gene Names: EFNB3 (EPLG8, LERK8)
Find proteins for Q15768 (Homo sapiens)
Go to Gene View: EFNB3
Go to UniProtKB:  Q15768
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.65 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.327 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 300.530α = 90.00
b = 300.530β = 90.00
c = 300.530γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2013-08-21
    Type: Database references
  • Version 1.3: 2015-11-11
    Type: Data collection
  • Version 1.4: 2019-04-03
    Type: Data collection, Other, Source and taxonomy