Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.87 kDa 
• Atom Count: 2338 
• Modelled Residue Count: 290 
• Deposited Residue Count: 306 
• Unique protein chains: 1

4GT5

Crystal structure of the inactive TrkA kinase domain

• DOI: 10.2210/pdb4GT5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-28 Released: 2012-09-26 
• Deposition Author(s): Artim, S.C., Lemmon, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family.

Artim, S.C., Mendrola, J.M., Lemmon, M.A.

(2012) Biochem J 448: 213-220

• PubMed: 22992069 
• DOI: 10.1042/BJ20121365
• Primary Citation of Related Structures:  
  4GT4, 4GT5


• PubMed Abstract: 
  

To investigate the range of autoinhibitory mechanisms used by TKDs (tyrosine kinase domains) from the insulin receptor family of RTKs (receptor tyrosine kinases), we determined crystal structures of TKDs from TrkA (tropomyosin receptor kinase A, a nerve growth factor receptor) and Ror2 (receptor tyrosine kinase-like orphan receptor 2, an unconventional Wnt receptor). TrkA autoinhibition closely resembles that seen for the insulin receptor, relying on projection of an activation loop tyrosine residue into the substrate-binding site and occlusion of the ATP-binding site by the activation loop. Ror2 employs similar mechanisms, but the unusual replacement of the phenylalanine residue in its Asp-Phe-Gly motif with leucine necessitates occlusion of the ATP-binding site by other means. The unusual Asp-Leu-Gly motif in Ror2 is displaced compared with other inactive kinases, allowing the activation loop to interact directly with the TKD's αC helix, in another mode of autoinhibition that is characteristic of the other extreme of this receptor family: ALK (anaplastic lymphoma kinase) and Met. These findings provide insight into the expected range of activating mutations in these TKDs in cancer. We also describe symmetrical dimers of the inactive TrkA TKD resembling those found in other RTKs, possibly reflecting an arrangement of kinase domains in a pre-formed TrkA dimer.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	306	Homo sapiens	Mutation(s): 0  Gene Names: MTC, NTRK1, TRK, TRKA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629  Go to UniProtKB:  P04629
PHAROS:  P04629

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.033	α = 90
b = 105.033	β = 90
c = 203.316	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-28 
• Released Date: 2012-09-26 
Deposition Author(s): Artim, S.C., Lemmon, M.A.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references
• Version 1.2: 2012-11-21
  Changes: Database references