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(-) Description

Title :  GLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT
 
Authors :  C. Eigenbrot, N. Gerber
Date :  25 Mar 97  (Deposition) - 05 Jun 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Growth Factor, Neurotrophic Factor, Cystine Knot (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Eigenbrot, N. Gerber
X-Ray Structure Of Glial Cell-Derived Neurotrophic Factor At 1. 9 A Resolution And Implications For Receptor Binding.
Nat. Struct. Biol. V. 4 435 1997
PubMed-ID: 9187648  |  Reference-DOI: 10.1038/NSB0697-435
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLIAL CELL-DERIVED NEUROTROPHIC FACTOR
    CellGLIA
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    OrganBRAIN
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGDNF

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1AGQ)

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:103
2A:69 -A:132
3A:73 -A:134
4A:102 -B:102
5B:42 -B:103
6B:69 -B:132
7B:73 -B:134
8C:42 -C:103
9C:69 -C:132
10C:73 -C:134
11C:102 -D:102
12D:42 -D:103
13D:69 -D:132
14D:73 -D:134

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AGQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1AGQ)

(-) 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:91
 aligned with GDNF_RAT | Q07731 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:97
                                   124       134       144       154       164       174       184       194       204       
             GDNF_RAT   115 NRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTSDKVGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 211
               SCOP domains d1agqa_ A: Glial cell-derived neurotrophic factor, GD      NF                                     SCOP domains
               CATH domains 1agqA00 A:39-135 Cystine-knot cytokines                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeehhhh........eeeeeeee........hhhhhhhhhhhh.------....eeeeee....eeee.....eeee......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1agq A  39 NRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSR------VGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 135
                                    48        58        68        78        88  |     98       108       118       128       
                                                                               91     98                                     

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with GDNF_RAT | Q07731 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:98
                                   123       133       143       153       163       173       183       193       203        
             GDNF_RAT   114 KNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTSDKVGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 211
               SCOP domains d1agqb_ B: Glial cell-derived neurotrophic factor, GDNF                                            SCOP domains
               CATH domains 1agqB00 B:38-135 Cystine-knot cytokines                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeehhhh........eeeeeeee........hhhhhhhhhhh......--....eeeeee....eeee.....eeee......eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1agq B  38 KNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTS--VGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 135
                                    47        57        67        77        87       | -|      107       117       127        
                                                                                    95 98                                     

Chain C from PDB  Type:PROTEIN  Length:91
 aligned with GDNF_RAT | Q07731 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:95
                                   126       136       146       156       166       176       186       196       206     
             GDNF_RAT   117 GCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTSDKVGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 211
               SCOP domains d1agqc_ C: Glial cell-derived neurotrophic factor, GD    NF                                     SCOP domains
               CATH domains 1agqC00 C:41-135 Cystine-knot cytokines                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhh........eeeeeeee........hhhhhhhhhhh....----....eeeeee....eeee.....eeee......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1agq C  41 GCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRL----VGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 135
                                    50        60        70        80        90  |    100       110       120       130     
                                                                               93   98                                     

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with GDNF_RAT | Q07731 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:95
                                   126       136       146       156       166       176       186       196       206     
             GDNF_RAT   117 GCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTSDKVGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 211
               SCOP domains d1agqd_ D: Glial cell-derived neurotrophic factor, GDNF                                         SCOP domains
               CATH domains 1agqD00 D:41-135 Cystine-knot cytokines                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhh........eeeeeeee........hhhhhhhhhhh.............eeeee....eeee.....eeee......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1agq D  41 GCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCEAAETMYDKILKNLSRSRRLTSDKVGQACCRPVAFDDDLSFLDDSLVYHILRKHSAKRCGCI 135
                                    50        60        70        80        90       100       110       120       130     

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GDNF_RAT | Q07731)
molecular function
    GO:0030116    glial cell-derived neurotrophic factor receptor binding    A growth factor that binds selectively and non-covalently to glial cell-derived neurotrophic factor receptors.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0001658    branching involved in ureteric bud morphogenesis    The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071549    cellular response to dexamethasone stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dexamethasone stimulus.
    GO:0048484    enteric nervous system development    The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation.
    GO:0048255    mRNA stabilization    Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0003337    mesenchymal to epithelial transition involved in metanephros morphogenesis    A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    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:0001755    neural crest cell migration    The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0030432    peristalsis    A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards.
    GO:0090190    positive regulation of branching involved in ureteric bud morphogenesis    Any process that increases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    GO:0032770    positive regulation of monooxygenase activity    Any process that activates or increases the activity of a monooxygenase.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0072107    positive regulation of ureteric bud formation    Any process that increases the rate or extent of the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct.
    GO:0021784    postganglionic parasympathetic fiber development    The process whose specific outcome is the progression of the postganglionic portion of the parasympathetic fiber over time, from its formation to the mature structure. The parasympathetic fiber is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia.
    GO:0051584    regulation of dopamine uptake involved in synaptic transmission    Any process that modulates the frequency, rate or extent of the directed movement of the catecholamine neurotransmitter dopamine into a cell.
    GO:0060688    regulation of morphogenesis of a branching structure    Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized.
    GO:0072106    regulation of ureteric bud formation    Any process that modulates the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0048485    sympathetic nervous system development    The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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