Database accession: MF2100007
Name: Neurotrophin 3 homodimer
PDB ID: 1b8k
Experimental method: X-ray (2.15 Å)
Assembly: homodimer
Source organism: Homo sapiens
Primer publication of the structure:
Robinson RC, Radziejewski C, Spraggon G, Greenwald J, Kostura MR, Burtnick LD, Stuart DI, Choe S, Jones EY
The structures of the neurotrophin 4 homodimer and the brain-derived neurotrophic factor/neurotrophin 4 heterodimer reveal a common Trk-binding site.
(1999) Protein Sci. 8: 2589-97
PMID: 10631974
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. 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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
neurotrophin p75 receptor binding Interacting selectively and non-covalently with the neurotrophin p75 receptor.
growth factor activity The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
nerve growth factor binding Interacting selectively and non-covalently with nerve growth factor (NGF).
chemoattractant activity Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
Biological process:
negative regulation of neuron apoptotic process Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
positive chemotaxis The directed movement of a motile cell or organism towards a higher concentration of a chemical.
negative regulation of peptidyl-tyrosine phosphorylation Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
induction of positive chemotaxis Any process that initiates the directed movement of a motile cell or organism towards a higher concentration in a concentration gradient of a specific chemical.
positive regulation of cell proliferation Any process that activates or increases the rate or extent of cell proliferation.
positive regulation of glial cell differentiation Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
activation of GTPase activity Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
activation of protein kinase B activity Any process that initiates the activity of the inactive enzyme protein kinase B.
neuron projection morphogenesis The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
positive regulation of receptor internalization Any process that activates or increases the frequency, rate or extent of receptor internalization.
positive regulation of actin cytoskeleton reorganization Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
positive regulation of peptidyl-serine phosphorylation Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
positive regulation of peptidyl-tyrosine phosphorylation Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
positive regulation of cell migration Any process that activates or increases the frequency, rate or extent of cell migration.
modulation of synaptic transmission Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
activation of MAPK activity The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
regulation of neuron differentiation Any process that modulates the frequency, rate or extent of neuron differentiation.
transmembrane receptor protein tyrosine kinase signaling pathway A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
Cellular component:
cytoplasmic, membrane-bounded vesicle A membrane-bounded vesicle found in the cytoplasm of the cell.
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: Chain B was generated from chain A using the biomatrices described in the original PDB file.
Number of unique protein segments: 1
Name: Neurotrophin-3
Source organism: Homo sapiens
Length: 119 residues
Sequence:Sequence according to PDB SEQRESYAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRKIGRT
UniProtKB AC: P20783 (positions: 139-257) Coverage: 46.3%
UniRef90 AC: UniRef90_P20783 (positions: 139-257)
Name: Neurotrophin-3
Source organism: Homo sapiens
Length: 119 residues
Sequence:Sequence according to PDB SEQRESYAEHKSHRGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRKIGRT
UniProtKB AC: P20783 (positions: 139-257) Coverage: 46.3%
UniRef90 AC: UniRef90_P20783 (positions: 139-257)
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Complex evidence:
Various dimeric members of neurotrophic factors (including human/mouse nerve growth factor, human brain-derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and neurotrophin 4/5 (NT-4/5)) have been shown to fold and dimerize at the same time via a two-state process (PMID: 8161524). While the members of this family show a significant variance in sequence, they adopt a highly similar structure upon binding and behave almost identically in unfolding/refolding experiments. Thus the two-state folding/binding nature seems to be a hallmark of NGF and closely related proteins.
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download our modified structure (.pdb)
