2X11 | pdb_00002x11

Crystal structure of the complete EphA2 ectodomain in complex with ephrin A5 receptor binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.83 Å
  • R-Value Free: 
    0.314 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.312 (Depositor), 0.304 (DCC) 
  • R-Value Observed: 
    0.313 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2X11

This is version 1.4 of the entry. See complete history

Literature

An Extracellular Steric Seeding Mechanism for Eph-Ephrin Signalling Platform Assembly

Seiradake, E.Harlos, K.Sutton, G.Aricescu, A.R.Jones, E.Y.

(2010) Nat Struct Mol Biol 17: 398

  • DOI: https://doi.org/10.1038/nsmb.1782
  • Primary Citation Related Structures: 
    2X10, 2X11

  • PubMed Abstract: 

    Erythropoetin-producing hepatoma (Eph) receptors are cell-surface protein tyrosine kinases mediating cell-cell communication. Upon activation, they form signaling clusters. We report crystal structures of the full ectodomain of human EphA2 (eEphA2) both alone and in complex with the receptor-binding domain of the ligand ephrinA5 (ephrinA5 RBD). Unliganded eEphA2 forms linear arrays of staggered parallel receptors involving two patches of residues conserved across A-class Ephs. eEphA2-ephrinA5 RBD forms a more elaborate assembly, whose interfaces include the same conserved regions on eEphA2, but rearranged to accommodate ephrinA5 RBD. Cell-surface expression of mutant EphA2s showed that these interfaces are critical for localization at cell-cell contacts and activation-dependent degradation. Our results suggest a 'nucleation' mechanism whereby a limited number of ligand-receptor interactions 'seed' an arrangement of receptors which can propagate into extended signaling arrays.


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

Macromolecule Content 

  • Total Structure Weight: 80.26 kDa 
  • Atom Count: 4,889 
  • Modeled Residue Count: 627 
  • Deposited Residue Count: 722 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EPHRIN TYPE-A RECEPTOR 2545Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000142627 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29317
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
EPHRIN-A5177Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P52803 (Homo sapiens)
Explore P52803 
Go to UniProtKB:  P52803
PHAROS:  P52803
GTEx:  ENSG00000184349 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52803
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.83 Å
  • R-Value Free:  0.314 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.312 (Depositor), 0.304 (DCC) 
  • R-Value Observed: 0.313 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.63α = 90
b = 59.63β = 90
c = 112.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2018-02-28
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary