1HE7

Human Nerve growth factor receptor TrkA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification and Structure of the Nerve Growth Factor Binding Site on Trka.

Robertson, A.G.S.Banfield, M.J.Allen, S.J.Dando, J.A.Mason, G.G.F.Tyler, S.J.Bennett, G.S.Brain, S.D.Clarke, A.R.Naylor, R.L.Wilcock, G.K.Brady, R.L.Dawbarn, D.

(2001) Biochem Biophys Res Commun 282: 131

  • DOI: 10.1006/bbrc.2001.4462
  • Primary Citation of Related Structures:  
    1HE7

  • PubMed Abstract: 
  • Nerve growth factor (NGF) is involved in the development and maintenance of the nervous system and has been implicated as a possible therapeutic target molecule in a number of neurodegenerative diseases, especially Alzheimer's disease. NGF binds with high affinity to the extracellular region of a tyrosine kinase receptor, TrkA, which comprises three leucine-rich motifs (LRMs), flanked by two cysteine-rich clusters, followed by two immunoglobulin-like (Ig-like) domains ...

    Nerve growth factor (NGF) is involved in the development and maintenance of the nervous system and has been implicated as a possible therapeutic target molecule in a number of neurodegenerative diseases, especially Alzheimer's disease. NGF binds with high affinity to the extracellular region of a tyrosine kinase receptor, TrkA, which comprises three leucine-rich motifs (LRMs), flanked by two cysteine-rich clusters, followed by two immunoglobulin-like (Ig-like) domains. We have expressed the second Ig-like domain as a recombinant protein in E. coli and demonstrate that NGF binds to this domain with similar affinity to the native receptor. This domain (TrkAIg(2)) has the ability to sequester NGF in vitro, preventing NGF-induced neurite outgrowth, and in vivo, inhibiting NGF-induced plasma extravasation. We also present the three-dimensional structure of the TrkAIg(2) domain in a new crystal form, refined to 2.0 A resolution.


    Related Citations: 
    • Crystal Structure of the Neurotrophin-Binding Domain of Trka, Trkb and Trkc
      Ultsch, M.H., Wiesmann, C., Simmons, L.C., Henrich, J., Yang, M., Reilly, D., Bass, S.H., De Vos, A.M.
      (1999) J Mol Biol 290: 149
    • Crystal Structure of Nerve Growth Factor in Complex with the Ligand-Binding Domain of the Trka Receptor
      Wiesmann, C., Ultsch, M.H., Bass, S.H., De Vos, A.M.
      (1999) Nature 401: 184

    Organizational Affiliation

    Molecular Neurobiology Unit, URCN, Bristol, BS2 8HW, United Kingdom. alan.robertson@bristol.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIGH AFFINITY NERVE GROWTH FACTOR RECEPTORA126Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.854α = 90
b = 50.854β = 90
c = 107.808γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-02
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection