1B8M

BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.198 

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
  • Primary Citation of Related Structures:  
    1B8K, 1B8M, 1B98

  • 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 of the target tissue ...

    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 (Slash)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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BRAIN DERIVED NEUROTROPHIC FACTOR)A119Homo sapiensMutation(s): 0 
Gene Names: BDNF
UniProt & NIH Common Fund Data Resources
Find proteins for P23560 (Homo sapiens)
Explore P23560 
Go to UniProtKB:  P23560
PHAROS:  P23560
GTEx:  ENSG00000176697 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23560
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (NEUROTROPHIN-4)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
GTEx:  ENSG00000225950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34130
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.7α = 90
b = 105.9β = 90
c = 51.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance