1HCF

Crystal structure of TrkB-d5 bound to neurotrophin-4/5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Specificity in Trk-Receptor:Neurotrophin Interaction: The Crystal Structure of Trkb-D5 in Complex with Neurotrophin-4/5

Banfield, M.J., Naylor, R.L., Robertson, A.G.S., Allen, S.J., Dawbarn, D., Brady, R.L.

(2001) Structure 9: 1191


  • PubMed Abstract: 

    • The binding of neurotrophin ligands to their respective Trk cellular receptors initiates intracellular signals essential for the growth and survival of neurons. The site of neurotrophin binding has been located to the fifth extracellular domain of th ...

    The binding of neurotrophin ligands to their respective Trk cellular receptors initiates intracellular signals essential for the growth and survival of neurons. The site of neurotrophin binding has been located to the fifth extracellular domain of the Trk receptor, with this region regulating both the affinity and specificity of Trk receptor:neurotrophin interaction. Neurotrophin function has been implicated in a number of neurological disorders, including Alzheimer's disease and Parkinson's disease.

    Related Citations: 
    • 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.,Devos, A.M.
      (1999) Nature 401: 184
    • 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.,Brady, R.L.,Dawbarn, D.
      (2001) Biochem.Biophys.Res.Commun. 282: 131
    • Crystal Structures 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.,Devos, A.M.
      (1999) J.Mol.Biol. 290: 149
    • The Structures of Neurotrophin 4 Homodimer and the Brain-Derived Neurotrophic Factor/Neurotrophin 4 Heterodimer Reveal a Common Trk Binding Site
      Robinson, R.C.,Radziejewski, C.,Spraggon, G.,Greenwald, J.,Kostura, M.R.,Burtnick, L.D.,Stuart, D.I.,Choe, S.,Jones, E.Y.
      (1999) Protein Sci. 8: 2589

    Organizational Affiliation: 

    Department of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUROTROPHIN-4
A, B
130Homo sapiensMutation(s): 0 
Gene Names: NTF4 (NTF5)
Find proteins for P34130 (Homo sapiens)
Go to Gene View: NTF4
Go to UniProtKB:  P34130
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BDNF/NT-3 GROWTH FACTORS RECEPTOR
X, Y
101Homo sapiensMutation(s): 0 
Gene Names: NTRK2 (TRKB)
EC: 2.7.10.1
Find proteins for Q16620 (Homo sapiens)
Go to Gene View: NTRK2
Go to UniProtKB:  Q16620
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.372α = 90.00
b = 80.406β = 90.00
c = 91.318γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance