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(-) Description

Title :  HUMAN NEUROTROPHIN-3
 
Authors :  M. J. Butte, P. K. Hwang, W. C. Mobley, R. J. Fletterick
Date :  17 May 99  (Deposition) - 06 Jun 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Neurotrophin, Growth Factor, Cystine Knot, Hormone-Growth Factor- Neuropeptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Butte, P. K. Hwang, W. C. Mobley, R. J. Fletterick
Crystal Structure Of Neurotrophin-3 Homodimer Shows Distinc Regions Are Used To Bind Its Receptors.
Biochemistry V. 37 16846 1998
PubMed-ID: 9836577  |  Reference-DOI: 10.1021/BI981254O

(-) Compounds

Molecule 1 - PROTEIN (NEUROTROPHIN-3)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NT-3, NT3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NT3)

(-) Sites  (0, 0)

(no "Site" information available for 1NT3)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:14 -A:79
2A:57 -A:108
3A:67 -A:110

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NT3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NT3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NGF_1PS00248 Nerve growth factor family signature.NTF3_HUMAN204-217  1A:66-79
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NGF_1PS00248 Nerve growth factor family signature.NTF3_HUMAN204-217  2A:66-79

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003310102aENSE00001740540chr12:5603311-56043441034NTF3_HUMAN1-2812811A:8-115108

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:108
 aligned with NTF3_HUMAN | P20783 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:108
                                   155       165       175       185       195       205       215       225       235       245        
           NTF3_HUMAN   146 RGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRK 253
               SCOP domains d1nt3a_ A: Neurotrophin 3, NT3                                                                               SCOP domains
               CATH domains 1nt3A00 A:8-115 Cystine-knot cytokines                                                                       CATH domains
               Pfam domains NGF-1nt3A01 A:8-115                                                                                          Pfam domains
         Sec.struct. author ........eeeeee....eee.....eee...............eeeeee..................eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------NGF_1         ------------------------------------ PROSITE
               Transcript 1 Exon 1.2a  PDB: A:8-115 UniProt: 1-281 [INCOMPLETE]                                                          Transcript 1
                 1nt3 A   8 RGEYSVCDSESLWVTDKSSAIDIRGHQVTVLGEIKTGNSPVKQYFYETRCKEARPVKNGCRGIDDKHWNSQCKTSQTYVRALTSENNKLVGWRWIRIDTSCVCALSRK 115
                                    17        27        37        47        57        67        77        87        97       107
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cystine-knot (56)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A   (NTF3_HUMAN | P20783)
molecular function
    GO:0042056    chemoattractant activity    Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
    GO:0008083    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.
    GO:0048406    nerve growth factor binding    Interacting selectively and non-covalently with nerve growth factor (NGF).
    GO:0005166    neurotrophin p75 receptor binding    Interacting selectively and non-covalently with the neurotrophin p75 receptor.
    GO:0005165    neurotrophin receptor binding    Interacting selectively and non-covalently with a neurotrophin receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0050930    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.
    GO:0050804    modulation of chemical 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.
    GO:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0043524    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.
    GO:0050732    negative regulation of peptidyl-tyrosine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0048812    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.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0045687    positive regulation of glial cell differentiation    Any process that activates or increases the frequency, rate or extent of glia cell differentiation.
    GO:0033138    positive regulation of peptidyl-serine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0002092    positive regulation of receptor internalization    Any process that activates or increases the frequency, rate or extent of receptor internalization.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007169    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
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NTF3_HUMAN | P20783: 1b8k 1bnd 3buk

(-) Related Entries Specified in the PDB File

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