1HCF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 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

  • DOI: 10.1016/s0969-2126(01)00681-5
  • Primary Citation of Related Structures:  
    1HCF

  • 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 the Trk receptor, with this region regulating both the affinity and specificity of Trk receptor:neurotrophin interaction ...

    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: 
    • 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 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
    • 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEUROTROPHIN-4A, B130Homo sapiensMutation(s): 0 
Gene Names: NTF4, NTF5
UniProt & NIH Common Fund Data Resources
Find proteins for P34130 (Homo sapiens)
Explore P34130 
Go to UniProtKB:  P34130
PHAROS:  P34130
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34130
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BDNF/NT-3 GROWTH FACTORS RECEPTORC [auth X],
D [auth Y]		101Homo sapiensMutation(s): 0 
Gene Names: NTRK2, TRKB
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16620 (Homo sapiens)
Explore Q16620 
Go to UniProtKB:  Q16620
PHAROS:  Q16620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16620
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.372α = 90
b = 80.406β = 90
c = 91.318γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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