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(-) Description

Title :  BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4
 
Authors :  R. C. Robinson, C. Radziejewski, D. I. Stuart, E. Y. Jones, S. Choe
Date :  01 Feb 99  (Deposition) - 09 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex (Growth Factor/Growth Factor), Neurotrophin, Growth Factor/Neurotrophin-4 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

Molecule 1 - PROTEIN (BRAIN DERIVED NEUROTROPHIC FACTOR)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSUPPLIED BY REGENERON PHARM.
    SynonymBDNF
 
Molecule 2 - PROTEIN (NEUROTROPHIN-4)
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSUPPLIED BY REGENERON PHARM.
    SynonymNT4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1B8M)

(-) Sites  (0, 0)

(no "Site" information available for 1B8M)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:13 -A:80
2A:58 -A:109
3A:68 -A:111
4B:17 -B:90
5B:61 -B:119
6B:78 -B:121

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063202R114GNTF4_HUMANPolymorphism377553005BR34G
2UniProtVAR_063203R133HNTF4_HUMANPolymorphism  ---BR53H
3UniProtVAR_063204R140CNTF4_HUMANPolymorphism201069064BR60C
4UniProtVAR_063205R206QNTF4_HUMANUnclassified (GLC1O)121918428BR126Q
5UniProtVAR_063206R206WNTF4_HUMANUnclassified (GLC1O)121918427BR126W
6UniProtVAR_063207T207INTF4_HUMANPolymorphism371861346BT127I
7UniProtVAR_063208T207SNTF4_HUMANPolymorphism  ---BT127S
8UniProtVAR_063209R209GNTF4_HUMANUnclassified (GLC1O)200675509BR129G

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NGF_1PS00248 Nerve growth factor family signature.NTF4_HUMAN157-170  1B:77-90
BDNF_HUMAN195-208  1A:67-80

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5ENST000003959835ENSE00001593506chr11:27722600-2772251883BDNF_HUMAN-00--
1.11fENST0000039598311fENSE00002153606chr11:27680132-276764403693BDNF_HUMAN1-2542541A:8-116109

(-) 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:109
 aligned with BDNF_HUMAN | P23560 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:109
                                   145       155       165       175       185       195       205       215       225       235         
           BDNF_HUMAN   136 GELSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIK 244
               SCOP domains d1b8ma_ A: Brain-derived neurotrophic factor, BDNF                                                            SCOP domains
               CATH domains 1b8mA00 A:8-116 Cystine-knot cytokines                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeehhhh.eee.....eee...eeee..eeee.eeeeeee..................eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------NGF_1         ------------------------------------ PROSITE
               Transcript 1 Exon 1.11f  PDB: A:8-116 UniProt: 1-254 [INCOMPLETE]                                                          Transcript 1
                 1b8m A   8 GELSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQYFYETKCNPMGYTKEGCRGIDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIK 116
                                    17        27        37        47        57        67        77        87        97       107         

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with NTF4_HUMAN | P34130 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:119
                                   101       111       121       131       141       151       161       171       181       191       201         
           NTF4_HUMAN    92 GELAVCDAVSGWVTDRRTAVDLRGREVEVLGEVPAAGGSPLRQYFFETRCKADNAEEGGPGAGGGGCRGVDRRHWVSECKAKQSYVRALTADAQGRVGWRWIRIDTACVCTLLSRTGRA 210
               SCOP domains d1b8mb_ B: Neurotrophin 4, NT4                                                                                          SCOP domains
               CATH domains 1b8mB00 B:12-130 Cystine-knot cytokines                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....eee.....eee................eeeeee..----...................eeeeeeeeeeeeeeee.....eeeeeeeee.eeeeeeee..... Sec.struct. author
             SAPs(SNPs) (1) ----------------------G------------------H------C-----------------------------------------------------------------QI-G- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------WS--- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------NGF_1         ---------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1b8m B  12 GELAVCDAVSGWVTDRRTAVDLRGREVEVLGEVPAAGGSPLRQYFFETRCKA----AGGPGAGGGGCRGVDRRHWVSECKAKQSYVRALTADAQGRVGWRWIRIDTACVCTLLSRTGRA 130
                                    21        31        41        51        61 |    | 71        81        91       101       111       121         
                                                                              63   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  (2, 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 1B8M)

(-) Gene Ontology  (31, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BDNF_HUMAN | P23560)
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:0005169    neurotrophin TRKB receptor binding    Interacting selectively and non-covalently with the neurotrophin TRKB receptor.
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0031547    brain-derived neurotrophic factor receptor signaling pathway    The series of molecular signals generated as a consequence of a brain-derived neurotrophic factor receptor binding to one of its physiological ligands.
    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:0048668    collateral sprouting    The process in which outgrowths develop from the shafts of existing axons.
    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: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:0031550    positive regulation of brain-derived neurotrophic factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling via the brain-derived neurotrophic factor receptor signaling pathway.
    GO:0048672    positive regulation of collateral sprouting    Any process that activates or increases the frequency, rate or extent of collateral sprouting.
    GO:0051965    positive regulation of synapse assembly    Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

Chain B   (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)

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        BDNF_HUMAN | P235601bnd
        NTF4_HUMAN | P341301b98 1hcf

(-) Related Entries Specified in the PDB File

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