1B98

NEUROTROPHIN 4 (HOMODIMER)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structures of the 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: 2589-2597

  • DOI: 10.1110/ps.8.12.2589
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The neurotrophins are growth factors that are involved in the development and survival of neurons. Neurotrophin release by a target tissue results in neuron growth along the neurotrophin concentration gradient, culminating in the eventual innervation ...

    The neurotrophins are growth factors that are involved in the development and survival of neurons. Neurotrophin release by a target tissue results in neuron growth along the neurotrophin concentration gradient, culminating in the eventual innervation of the target tissue. These activities are mediated through trk cell surface receptors. We have determined the structures of the heterodimer formed between brain-derived neurotrophic factor (BDNF) and neurotrophin 4 (NT4), as well as the structure of homodimer of NT4. We also present the structure of the Neurotrophin 3 homodimer, which is refined to higher resolution than previously published. These structures provide the first views of the architecture of the NT4 protomer. Comparison of the surface of a model of the BDNF homodimer with the structures of the neurotrophin homodimers reveals common features that may be important in the binding between the neurotrophins and their receptors. In particular, there exists an analogous region on the surface of each neurotrophin that is likely to be involved in trk receptor binding. Variations in sequence on the periphery of this common region serve to confer trk receptor specificity.


    Related Citations: 
    • Structure of the Brain-Derived Neurotrophic Factor/Neurotrophin 3 Heterodimer
      Robinson, R.C., Radziejewski, C., Stuart, D.I., Jones, E.Y.
      (1995) Biochemistry 34: 4139
    • Heterodimers of the Neurotrophic Factors: Formation, Isolation, and Differential Stability
      Radziejewski, C., Robinson, R.C.
      (1993) Biochemistry 32: 13350

    Organizational Affiliation

    Structural Biology Laboratory, The Salk Institute, La Jolla, California 92037, USA. bob@sbl.salk.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NEUROTROPHIN-4)
A, M
130Homo sapiensMutation(s): 0 
Gene Names: NTF4NTF5
Find proteins for P34130 (Homo sapiens)
Go to UniProtKB:  P34130
NIH Common Fund Data Resources
PHAROS  P34130
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.8α = 90
b = 50.8β = 109.4
c = 53γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance