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(-) Description

Title :  SOLUTION STRUCTURE OF THE DROSOPHILA ARGONAUTE 1 PAZ DOMAIN
 
Authors :  K. S. Yan, S. Yan, A. Farooq, A. Han, L. Zeng, M. -M. Zhou
Date :  07 Oct 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Beta Barrel, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. S. Yan, S. Yan, A. Farooq, A. Han, L. Zeng, M. -M. Zhou
Structure And Conserved Rna Binding Of The Paz Domain
Nature V. 426 468 2003
PubMed-ID: 14615802  |  Reference-DOI: 10.1038/NATURE02129
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGONAUTE 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET19B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPAZ DOMAIN
    GeneAGO1
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R4K)

(-) Sites  (0, 0)

(no "Site" information available for 1R4K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R4K)

(-) Exons   (0, 0)

(no "Exon" information available for 1R4K)

(-) 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:168
 aligned with Q32KD4_DROME | Q32KD4 from UniProtKB/TrEMBL  Length:984

    Alignment length:168
                                   340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490        
         Q32KD4_DROME   331 TAFYKAQPVIDFMCEVLDIRDINEQRKPLTDSQRVKFTKEIKGLKIEITHCGQMRRKYRVCNVTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYRMKLRYPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREINNLVKRADFN 498
               SCOP domains d1r4ka_ A: Argonaute 1                                                                                                                                                   SCOP domains
               CATH domains 1r4kA01 A:297-428 paz domain                                                                                                        ------------------------------------ CATH domains
               Pfam domains DUF178-------PAZ-1r4kA02 A:310-446                                                                                                                    ------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhh............hhhhhhhhhhhh...eeeee......eeee..eee..hhhheeeeeee...eeeeeee.hhhhhh...........eeee......eee...eeeee.......................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r4k A 297 TAFYKAQPVIDFMCEVLDIRDINEQRKPLTDSQRVKFTKEIKGLKIEITHCGQMRRKYRVCNVTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYRMKLRYPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREINNLVKRADFN 464
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456        

   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

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

NMR Structure

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (Q32KD4_DROME | Q32KD4)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0035198    miRNA binding    Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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).
biological process
    GO:0016246    RNA interference    The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0036099    female germ-line stem cell population maintenance    The process by which an organism or tissue maintains a population of female germ-line stem cells.
    GO:0035195    gene silencing by miRNA    Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.
    GO:0030727    germarium-derived female germ-line cyst formation    Formation, in a germarium, of a group of interconnected cells derived from a single female gonial founder cell (a cystoblast). The germarium is the most anterior portion of an insect ovariole. An example of this process is found in Drosophila melanogaster.
    GO:0007294    germarium-derived oocyte fate determination    The cell fate determination process in which a germarium-derived cell becomes capable of differentiating autonomously into an oocyte cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this is found in Drosophila melanogaster.
    GO:0046959    habituation    A decrease in a behavioral response to a repeated stimulus. This is exemplified by the failure of a person to show a startle response to a loud noise that has been repeatedly presented.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0035279    mRNA cleavage involved in gene silencing by miRNA    The process in which microRNAs (miRNAs) direct the cleavage of target mRNAs. Once incorporated into a RNA-induced silencing complex (RISC), a miRNA base pairing with near-perfect complementarity to the target mRNA will typically direct targeted endonucleolytic cleavage of the mRNA. Many plant miRNAs downregulate gene expression through this mechanism.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0035196    production of miRNAs involved in gene silencing by miRNA    Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
    GO:0030422    production of siRNA involved in RNA interference    Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
    GO:0090328    regulation of olfactory learning    Any process that modulates the rate, frequency, or extent of olfactory learning. Olfactory learning is any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue.
    GO:0007367    segment polarity determination    Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products.
    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).
    GO:0030423    targeting of mRNA for destruction involved in RNA interference    The process in which small interfering RNAs target cognate mRNA molecules for degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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