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(-) Description

Title :  THE CRYSTAL STRUCTURE OF GDNF FAMILY CO-RECEPTOR ALPHA 1 DOMAIN 3
 
Authors :  V. M. Leppanen, M. M. Bespalov, P. Runeberg-Roos, U. Puurand, A. Merits, M. Saarma, A. Goldman
Date :  21 Aug 03  (Deposition) - 31 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  All-Alpha, Cys-Rich, Hormone/Growth Factor Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. Leppanen, M. M. Bespalov, P. Runeberg-Roos, U. Puurand, A. Merits, M. Saarma, A. Goldman
The Structure Of Gfralpha1 Domain 3 Reveals New Insights Into Gdnf Binding And Ret Activation.
Embo J. V. 23 1452 2004
PubMed-ID: 15044950  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600174
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GDNF FAMILY RECEPTOR ALPHA 1
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPFASTBAC
    Expression System Vector TypeBACULOVIRUS
    FragmentDOMAIN 3
    GeneGFRA1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGFR-ALPHA 1, GDNF RECEPTOR ALPHA, GDNFR-ALPHA, TGF-BETA RELATED NEUROTROPHIC FACTOR RECEPTOR 1, RET LIGAND 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:254 , SER A:290 , CYS A:315 , SER A:316 , LEU A:322 , HOH A:432BINDING SITE FOR RESIDUE MPD A 400

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:243 -A:313
2A:250 -A:256
3A:267 -A:285
4A:277 -A:337
5A:315 -A:325

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q8D)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q8D)

(-) 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:100
 aligned with GFRA1_RAT | Q62997 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:108
                                   248       258       268       278       288       298       308       318       328       338        
            GFRA1_RAT   239 ERPNCLSLQDSCKTNYICRSRLADFFTNCQPESRSVSNCLKENYADCLLAYSGLIGTVMTPNYVDSSSLSVAPWCDCSNSGNDLEDCLKFLNFFKDNTCLKNAIQAFG 346
               SCOP domains d1q8da_ A: GDNF receptor alpha                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----GDNF-1q8dA01 A:243-337                                                                         --------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.........--------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1q8d A 239 ERPNCLSLQDSCKTNYICRSRLADFFTNCQPESRSVSNCLKENYADCLLAYSGLIGTVmTPN--------VAPWCDCSNSGNDLEDCLKFLNFFKDNTCLKNAIQAFG 346
                                   248       258       268       278       288       298 |       -|      318       328       338        
                                                                                    297-MSE     309                                     
                                                                                       300                                              

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  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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Q8D)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GFRA1_RAT | Q62997)
molecular function
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    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: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).
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        GFRA1_RAT | Q629972v5e 3fub 4ux8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Q8D)