1JPA | pdb_00001jpa

Crystal Structure of unphosphorylated EphB2 receptor tyrosine kinase and juxtamembrane region

• PDB DOI: https://doi.org/10.2210/pdb1JPA/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2001-08-01 Released: 2001-10-03 
• Deposition Author(s): Wybenga-Groot, L.E., Pawson, T., Sicheri, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structural basis for autoinhibition of the Ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region.

Wybenga-Groot, L.E., Baskin, B., Ong, S.H., Tong, J., Pawson, T., Sicheri, F.

(2001) Cell 106: 745-757

• PubMed: 11572780 
• DOI: https://doi.org/10.1016/s0092-8674(01)00496-2
• Primary Citation Related Structures: 
  1JPA


• PubMed Abstract: 
  

  The Eph receptor tyrosine kinase family is regulated by autophosphorylation within the juxtamembrane region and the kinase activation segment. We have solved the X-ray crystal structure to 1.9 A resolution of an autoinhibited, unphosphorylated form of EphB2 comprised of the juxtamembrane region and the kinase domain. The structure, supported by mutagenesis data, reveals that the juxtamembrane segment adopts a helical conformation that distorts the small lobe of the kinase domain, and blocks the activation segment from attaining an activated conformation. Phosphorylation of conserved juxtamembrane tyrosines would relieve this autoinhibition by disturbing the association of the juxtamembrane segment with the kinase domain, while liberating phosphotyrosine sites for binding SH2 domains of target proteins. We propose that the autoinhibitory mechanism employed by EphB2 is a more general device through which receptor tyrosine kinases are controlled.

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Organizational Affiliation: 
• Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Ontario M5G 1X5, Toronto, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.66 kDa 
• Atom Count: 4,641 
• Modeled Residue Count: 542 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
neural kinase, Nuk=Eph/Elk/Eck family receptor-like tyrosine kinase	A, B	312	Mus musculus	Mutation(s): 2  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54763 (Mus musculus) Explore P54763  Go to UniProtKB:  P54763
IMPC:  MGI:99611

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A], D [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.052	α = 112.95
b = 57.616	β = 103.17
c = 67.742	γ = 91.58

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-03 
Deposition Author(s): Wybenga-Groot, L.E., Pawson, T., Sicheri, F.

Revision History  

• Version 1.0: 2001-10-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description