Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.58 kDa 
• Atom Count: 2018 
• Residue Count: 256 
• Unique protein chains: 1

2HEL

Crystal structure of a mutant EphA4 kinase domain (Y742A)

• DOI: 10.2210/pdb2HEL/pdb

• Classification: SIGNALING PROTEIN, TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-06-21 Released: 2007-02-13 
• Deposition Author(s): Wybenga-Groot, L.E., Sicheri, F., Pawson, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.209 

Literature

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

• PubMed: 16977320 
• DOI: 10.1038/sj.emboj.7601315
• Primary Citation of Related Structures:  
  2HEN, 2HEL


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eph receptor A4	A	306	Mus musculus	Mutation(s): 3  Gene Names: Epha4, Sek, Sek1 EC: 2.7.10.1
Find proteins for Q03137 (Mus musculus) Explore Q03137  Go to UniProtKB:  Q03137

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.248 
• R-Value Work: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.283	α = 90
b = 101.081	β = 108.8
c = 40.95	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-21 
• Released Date: 2007-02-13 
Deposition Author(s): Wybenga-Groot, L.E., Sicheri, F., Pawson, T.

Revision History 

• 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