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(-) Description

Authors :  R. C. Robinson, C. Radziejewski, D. I. Stuart, E. Y. Jones, S. Choe
Date :  22 Feb 99  (Deposition) - 26 Feb 99  (Release) - 24 Feb 09  (Revision)
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,M
Keywords :  Target-Derived Survival Factor, Neurotrophin 4, Neurotrophin 5, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  R. C. Robinson, C. Radziejewski, G. Spraggon, J. Greenwald, M. R. Kostura, L. D. Burtnick, D. I. Stuart, S. Choe, E. Y. Jones
The Structures Of The Neurotrophin 4 Homodimer And The Brain-Derived Neurotrophic Factor/Neurotrophin 4 Heterodimer Reveal A Common Trk-Binding Site.
Protein Sci. V. 8 2589 1999
PubMed-ID: 10631974
(for further references see the PDB file header)

(-) Compounds

    ChainsA, M
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPRECURSOR RESIDUES 81-210
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit AM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
1A:17 -A:90
2A:61 -A:119
3A:78 -A:121
4M:17 -M:90
5M:61 -M:119
6M:78 -M:121

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
2UniProtVAR_063203R133HNTF4_HUMANPolymorphism  ---A/MR53H
4UniProtVAR_063205R206QNTF4_HUMANUnclassified (GLC1O)121918428A/MR126Q
5UniProtVAR_063206R206WNTF4_HUMANUnclassified (GLC1O)121918427A/MR126W
7UniProtVAR_063208T207SNTF4_HUMANPolymorphism  ---AT127S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
1NGF_1PS00248 Nerve growth factor family signature.NTF4_HUMAN157-170

(-) Exons   (0, 0)

(no "Exon" information available for 1B98)

(-) Sequences/Alignments

Asymmetric/Biological 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:103
 aligned with NTF4_HUMAN | P34130 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:115
                                   102       112       122       132       142       152       162       172       182       192       202     
               SCOP domains d1b98a_ A: Neurotrophin 4, NT4                                                                                      SCOP domains
               CATH domains 1b98A00 A:13-127 Cystine-knot cy       tokines                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....eee.....eeee....-------....eeeeee..........................eeeeeeeeeeeeeee-----.eeeeeeeeeeeeeee.... Sec.struct. author
             SAPs(SNPs) (1) ---------------------G------------------H------C-----------------------------------------------------------------QI SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------WS SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------NGF_1         ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                                    22        32        42 |      52        62        72        82        92       102     | 112       122     
                                                          44      52                                               102   108                   

Chain M from PDB  Type:PROTEIN  Length:113
 aligned with NTF4_HUMAN | P34130 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:116
                                   100       110       120       130       140       150       160       170       180       190       200      
               SCOP domains d1b98m_ M: Neurotrophin 4, NT4                                                                                       SCOP domains
               CATH domains 1b98M00 M:11-126 Cystine-knot cytokines                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
             SAPs(SNPs) (1) -----------------------G------------------H------C-----------------------------------------------------------------Q SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------W SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------NGF_1         ------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                                    20        30        40        50        60   |   |70        80        90       100       110       120      
                                                                                64  68                                                          

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B98)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,M   (NTF4_HUMAN | P34130)
molecular function
    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:0005166    neurotrophin p75 receptor binding    Interacting selectively and non-covalently with the neurotrophin p75 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:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    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:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0007402    ganglion mother cell fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a ganglion mother cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    GO:0060384    innervation    The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0042490    mechanoreceptor differentiation    The process in which a relatively unspecialized cell acquires specialized features of a mechanoreceptor, a cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    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: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:0045664    regulation of neuron differentiation    Any process that modulates the frequency, rate or extent of neuron differentiation.
    GO:0008052    sensory organ boundary specification    The process in which boundaries between a sensory organ and the surrounding tissue are established and maintained.
    GO:0061193    taste bud development    The progression of the taste bud over time, from its formation to the mature state. The taste bud is a specialized area of the tongue that contains taste receptors.
    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:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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)

        NTF4_HUMAN | P341301b8m 1hcf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B98)