4L0P

Structure of the human EphA3 receptor ligand binding domain complexed with ephrin-A5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Distinctive Structure of the EphA3/Ephrin-A5 Complex Reveals a Dual Mode of Eph Receptor Interaction for Ephrin-A5.

Forse, G.J.Uson, M.L.Nasertorabi, F.Kolatkar, A.Lamberto, I.Pasquale, E.B.Kuhn, P.

(2015) Plos One 10: e0127081-e0127081

  • DOI: 10.1371/journal.pone.0127081

  • PubMed Abstract: 
  • The Eph receptor tyrosine kinase/ephrin ligand system regulates a wide spectrum of physiological processes, while its dysregulation has been implicated in cancer progression. The human EphA3 receptor is widely upregulated in the tumor microenvironmen ...

    The Eph receptor tyrosine kinase/ephrin ligand system regulates a wide spectrum of physiological processes, while its dysregulation has been implicated in cancer progression. The human EphA3 receptor is widely upregulated in the tumor microenvironment and is highly expressed in some types of cancer cells. Furthermore, EphA3 is among the most highly mutated genes in lung cancer and it is also frequently mutated in other cancers. We report the structure of the ligand-binding domain of the EphA3 receptor in complex with its preferred ligand, ephrin-A5. The structure of the complex reveals a pronounced tilt of the ephrin-A5 ligand compared to its orientation when bound to the EphA2 and EphB2 receptors and similar to its orientation when bound to EphA4. This tilt brings an additional area of ephrin-A5 into contact with regions of EphA3 outside the ephrin-binding pocket thereby enlarging the size of the interface, which is consistent with the high binding affinity of ephrin-A5 for EphA3. This large variation in the tilt of ephrin-A5 bound to different Eph receptors has not been previously observed for other ephrins.


    Organizational Affiliation

    Dornsife College of Letters, Arts and Sciences, University of Southern California, 3430 S. Vermont Ave., Suite 105 (110), MC3301, Los Angeles, CA, 90089-3301, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 3
A
176Homo sapiensMutation(s): 0 
Gene Names: EPHA3 (ETK, ETK1, HEK, TYRO4)
EC: 2.7.10.1
Find proteins for P29320 (Homo sapiens)
Go to Gene View: EPHA3
Go to UniProtKB:  P29320
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ephrin-A5
B
143Homo sapiensMutation(s): 0 
Gene Names: EFNA5 (EPLG7, LERK7)
Find proteins for P52803 (Homo sapiens)
Go to Gene View: EFNA5
Go to UniProtKB:  P52803
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.187 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 60.043α = 90.00
b = 60.043β = 90.00
c = 91.574γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
HKL-2000data scaling
Blu-Icedata collection
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Other
  • Version 1.2: 2015-07-01
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description