Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.26 kDa 
• Atom Count: 4889 
• Modelled Residue Count: 627 
• Deposited Residue Count: 722 
• Unique protein chains: 2

2X11

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

• PDB DOI: 10.2210/pdb2X11/pdb

• Classification: RECEPTOR/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2009-12-21 Released: 2010-03-16 
• Deposition Author(s): Seiradake, E., Harlos, K., Sutton, G., Aricescu, A.R., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.83 Å
• R-Value Free: 0.314 
• R-Value Work: 0.312 
• R-Value Observed: 0.313 

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

• PubMed: 20228801 
• DOI: 10.1038/nsmb.1782
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR 2	A	545	Homo sapiens	Mutation(s): 0  Gene Names: EPHA2, ECK 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN-A5	B	177	Homo sapiens	Mutation(s): 0  Gene Names: EFNA5, EPLG7, LERK7
UniProt & NIH Common Fund Data Resources
Find proteins for P52803 (Homo sapiens) Explore P52803  Go to UniProtKB:  P52803
PHAROS:  P52803

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.83 Å
• R-Value Free: 0.314 
• R-Value Work: 0.312 
• R-Value Observed: 0.313 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.63	α = 90
b = 59.63	β = 90
c = 112.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-21 
• Released Date: 2010-03-16 
Deposition Author(s): Seiradake, E., Harlos, K., Sutton, G., Aricescu, A.R., Jones, E.Y.

Revision History  

• 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