Crystal Structure of the EphB2 Receptor Kinase domain in complex with ADP

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases

Wiesner, S.Wybenga-Groot, L.E.Warner, N.Lin, H.Pawson, T.Forman-Kay, J.D.Sicheri, F.

(2006) EMBO J 25: 4686-4696

  • DOI: https://doi.org/10.1038/sj.emboj.7601315
  • Primary Citation of Related Structures:  
    2HEL, 2HEN

  • PubMed Abstract: 

    Eph receptor tyrosine kinases (RTKs) mediate numerous developmental processes. Their activity is regulated by auto-phosphorylation on two tyrosines within the juxtamembrane segment (JMS) immediately N-terminal to the kinase domain (KD). Here, we probe the molecular details of Eph kinase activation through mutational analysis, X-ray crystallography and NMR spectroscopy on auto-inhibited and active EphB2 and EphA4 fragments. We show that a Tyr750Ala gain-of-function mutation in the KD and JMS phosphorylation independently induce disorder of the JMS and its dissociation from the KD. Our X-ray analyses demonstrate that this occurs without major conformational changes to the KD and with only partial ordering of the KD activation segment. However, conformational exchange for helix alphaC in the N-terminal KD lobe and for the activation segment, coupled with increased inter-lobe dynamics, is observed upon kinase activation in our NMR analyses. Overall, our results suggest that a change in inter-lobe dynamics and the sampling of catalytically competent conformations for helix alphaC and the activation segment rather than a transition to a static active conformation underlies Eph RTK activation.

  • Organizational Affiliation

    Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ephrin type-B receptor 2
A, B, C, D
286Mus musculusMutation(s): 1 
Gene Names: Ephb2Epth3NukSek3
UniProt & NIH Common Fund Data Resources
Find proteins for P54763 (Mus musculus)
Explore P54763 
Go to UniProtKB:  P54763
IMPC:  MGI:99611
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54763
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.798α = 90
b = 98.304β = 90.18
c = 114.168γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection