Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 14.01 kDa 
• Atom Count: 938 
• Modelled Residue Count: 108 
• Deposited Residue Count: 126 
• Unique protein chains: 1

 1HE7

Human Nerve growth factor receptor TrkA

• PDB DOI:  https://doi.org/10.2210/pdb1HE7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2000-11-20 Released: 2001-04-02 
• Deposition Author(s): Banfield, M., Robertson, A., Allen, S., Dando, J., Tyler, S., Bennett, G., Brain, S., Mason, G., Holden, P., Clarke, A., Naylor, R., Wilcock, G., Brady, R., Dawbarn, D.

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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 

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

• PubMed: 11263982 
• DOI: https://doi.org/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. 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.

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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

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Organizational Affiliation: 

Molecular Neurobiology Unit, URCN, Bristol, BS2 8HW, United Kingdom. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR	A	126	Homo sapiens	Mutation(s): 0  Gene Names: NTRK1, MTC, TRK, TRKA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 50.854	α = 90
b = 50.854	β = 90
c = 107.808	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-02 
Deposition Author(s): Banfield, M., Robertson, A., Allen, S., Dando, J., Tyler, S., Bennett, G., Brain, S., Mason, G., Holden, P., Clarke, A., Naylor, R., Wilcock, G., Brady, R., Dawbarn, D.

Revision History  

• 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