7EED

Crystal structure of EphA7 mutant D751H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of clinically reported mutations Gly656Arg, Gly656Glu and Asp751His identified in the kinase domain of EphA7.

Chakraborty, S.Varma, A.K.

(2021) Biochem Biophys Res Commun 568: 62-67

  • DOI: https://doi.org/10.1016/j.bbrc.2021.06.048
  • Primary Citation of Related Structures:  
    7EEC, 7EED, 7EEF

  • PubMed Abstract: 

    Erythropoietin producing hepatocellular (Eph) forms the largest family of receptor tyrosine kinases (RTK). As a family, Eph regulates physiological events such as cell-cell interaction, cell migration, and adhesion. The Kinase domain is the catalytic core of the Eph receptor and is highly conserved sequentially. EphA7 has been recently regarded as a cancer driver gene and comprises several clinically important mutations. Three of the EphA7 mutations Gly656Glu, Gly656Arg, and Asp751His, present in the kinase domain, are predicted to be highly pathogenic. Furthermore, Gly656Glu and Gly656Arg are reported to be hotspot mutations. Considering the importance of mutations, crystals structure of EphA7 Gly656Glu, Gly656Arg, and Asp751His mutants has been explored. Changes in folding pattern and intramolecular interactions were observed in mutant structures. Secondary structural changes were observed in the hinge region of EphA7 Gly656Arg and Asp751His structure, affecting the transition of kinase domain between open and closed conformations. EphA7 Asp751His mutant structure shows a distorted nucleotide-binding groove. Differences were observed in hydrogen bonding and hydrophobic interactions between the catalytic and highly conserved DFG motif in the EphA7 mutants, which may influence the catalytic activity of kinase domain.


  • Organizational Affiliation

    Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ephrin type-A receptor 7304Homo sapiensMutation(s): 1 
Gene Names: EPHA7EHK3HEK11
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15375 (Homo sapiens)
Explore Q15375 
Go to UniProtKB:  Q15375
PHAROS:  Q15375
GTEx:  ENSG00000135333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15375
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.24α = 90
b = 51.24β = 90
c = 215.271γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description