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(-) Description

Title :  NMR STRUCTURE OF THE COMPLEX BETWEEN THE THIRD DSRBD FROM DROSOPHILA STAUFEN AND A RNA HAIRPIN
 
Authors :  A. Ramos, S. Grunert, M. Bycroft, D. St Johnston, G. Varani
Date :  11 Mar 00  (Deposition) - 21 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (36x)
Keywords :  Nmr Structure, Protein/Rna, Protein Dsrbd, Drosophila, Rna Hairpin, Cell Cycle/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ramos, S. Grunert, J. Adams, D. R. Micklem, M. R. Proctor, S. Freund, M. Bycroft, D. St Johnston, G. Varani
Rna Recognition By A Staufen Double-Stranded Rna-Binding Domain.
Embo J. V. 19 997 2000
PubMed-ID: 10698941  |  Reference-DOI: 10.1093/EMBOJ/19.5.997
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MATERNAL EFFECT PROTEIN (STAUFEN)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: DSRBDIII
 
Molecule 2 - STAUFEN DOUBLE-STRANDED RNA BINDING DOMAIN
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (36x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1EKZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EKZ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.STAU_DROME311-378
524-557
578-645
711-781
951-1018		  1-
-
A:8-75
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1EKZ)

(-) Sequences/Alignments

NMR Structure
   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:76
 aligned with STAU_DROME | P25159 from UniProtKB/Swiss-Prot  Length:1026

    Alignment length:76
                                   580       590       600       610       620       630       640      
           STAU_DROME   571 MDEGDKKSPISQVHEIGIKRNMTVHFKVLREEGPAHMKNFITACIVGSIVTEGEGNGKKVSKKRAAEKMLVELQKL 646
               SCOP domains d1ekza_ A: Staufen, domain III                                               SCOP domains
               CATH domains 1ekzA00 A:1-76  [code=3.30.160.20, no name defined]                          CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh....eeee.............eeeee..eeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DS_RBD  PDB: A:8-75 UniProt: 578-645                                - PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1ekz A   1 MDEGDKKSPISQVHEIGIKRNMTVHFKVLREEGPAHMKNFITACIVGSIVTEGEGNGKKVSKKRAAEKMLVELQKL  76
                                    10        20        30        40        50        60        70      


Chain B from PDB  Type:RNA  Length:30
                                                              
                 1ekz B   1 GGACAGCUGUCCCUUCGGGGACAGCUGUCC  30
                                    10        20        30
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 39)

NMR Structure(hide GO term definitions)
Chain A   (STAU_DROME | P25159)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
biological process
    GO:0006403    RNA localization    A process in which RNA is transported to, or maintained in, a specific location.
    GO:0008595    anterior/posterior axis specification, embryo    The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
    GO:0055059    asymmetric neuroblast division    The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
    GO:0045167    asymmetric protein localization involved in cell fate determination    Any process in which a protein is transported to, or maintained in, a specific asymmetric distribution, resulting in the formation of daughter cells of different types.
    GO:0045450    bicoid mRNA localization    Any process in which bicoid mRNA is transported to and maintained within the oocyte as part of the specification of the anterior/posterior axis.
    GO:0008298    intracellular mRNA localization    Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
    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:0007017    microtubule-based process    Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0007400    neuroblast fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0007316    pole plasm RNA localization    Any process in which RNA is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
    GO:0007315    pole plasm assembly    Establishment of the specialized cytoplasm found at the poles of the egg. An example of this is found in Drosophila melanogaster.
    GO:0019094    pole plasm mRNA localization    Any process in which mRNA is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
    GO:0045451    pole plasm oskar mRNA localization    Any process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
    GO:0007318    pole plasm protein localization    Any process in which a protein is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
    GO:0010606    positive regulation of cytoplasmic mRNA processing body assembly    Any process that increases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0046012    positive regulation of oskar mRNA translation    Any process that activates or increases the frequency, rate or extent of oskar mRNA translation.
    GO:0045887    positive regulation of synaptic growth at neuromuscular junction    Any process that activates or increases the frequency, rate or extent of synaptic growth at neuromuscular junction.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0035418    protein localization to synapse    Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell.
    GO:0046011    regulation of oskar mRNA translation    Any process that modulates the frequency, rate or extent of oskar mRNA translation. To ensure the localization of Oskar protein at the posterior pole of the oocyte, translation of oskar mRNA is repressed during its transport to the posterior pole and activated upon localization of the mRNA at the posterior cortex.
    GO:0007317    regulation of pole plasm oskar mRNA localization    Any process that modulates the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0045180    basal cortex    The region that lies just beneath the plasma membrane on the basal edge of a cell.
    GO:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0060293    germ plasm    Differentiated cytoplasm associated with a pole of an oocyte, egg or early embryo that will be inherited by the cells that will give rise to the germ line.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0071212    subsynaptic reticulum    An elaborate tubulolamellar membrane system that underlies the postsynaptic cell membrane.

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        STAU_DROME | P25159: 1stu 5cff

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