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(-) Description

Title :  STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1
 
Authors :  N. Mathioudakis, A. Palencia, J. Kadlec, A. Round, K. Tripsianes, M. Sa R. S. Pillai, S. Cusack
Date :  08 Sep 12  (Deposition) - 17 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Mathioudakis, A. Palencia, J. Kadlec, A. Round, K. Tripsianes, M. Sattler, R. S. Pillai, S. Cusack
The Multiple Tudor Domain-Containing Protein Tdrd1 Is A Molecular Scaffold For Mouse Piwi Proteins And Pirna Biogenesis Factors.
Rna V. 18 2056 2012
PubMed-ID: 22996915  |  Reference-DOI: 10.1261/RNA.034181.112

(-) Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorPETM11
    Expression System Vector TypePLASMID
    FragmentEXTENDED TUDOR DOMAIN TD3, RESIDUES 692-917
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTDRD1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4B9X)

(-) Sites  (0, 0)

(no "Site" information available for 4B9X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4B9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B9X)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.TDRD1_MOUSE307-367
536-595
756-815
982-1040
  1-
-
A:756-815
-

(-) Exons   (0, 0)

(no "Exon" information available for 4B9X)

(-) 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:194
 aligned with TDRD1_MOUSE | Q99MV1 from UniProtKB/Swiss-Prot  Length:1172

    Alignment length:196
                                   706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      
          TDRD1_MOUSE   697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh.....--.......eeeeee....eeeeeeeeee....eeeee......eeeee...ee..hhhhh......eeeee..ee......hhhhhhhhhhhhh...eeeeeeee....eeeeeee........hhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------TUDOR  PDB: A:756-815 UniProt: 756-815                      ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9x A 697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPP--FKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
                                   706       716       726       736       746     | 756       766       776       786       796       806       816       826       836       846       856       866       876       886      
                                                                                 752  |                                                                                                                                         
                                                                                    755                                                                                                                                         

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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  (0, 0)

(no "SCOP Domain" information available for 4B9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B9X)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TDRD1_MOUSE | Q99MV1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0043046    DNA methylation involved in gamete generation    The covalent transfer of a methyl group to C-5 of cytosine that contributes to the establishment of DNA methylation patterns in the gamete.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0007281    germ cell development    The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    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:0034587    piRNA metabolic process    The chemical reactions and pathways involving piRNAs, Piwi-associated RNAs, a class of 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0043186    P granule    A small cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.
    GO:0033391    chromatoid body    A ribonucleoprotein complex found in the cytoplasm of male germ cells, composed of exceedingly thin filaments that are consolidated into a compact mass or into dense strands of varying thickness that branch to form an irregular network. Contains mRNAs, miRNAs, and protein components involved in miRNA processing (such as Argonaute proteins and the endonuclease Dicer) and in RNA decay (such as the decapping enzyme DCP1a and GW182).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0071546    pi-body    A P granule that contains the PIWIL2-TDRD1 module, a set of proteins that act in the primary piRNA pathway. The pi-body corresponds to the cementing material between mitochondria found in gonocytes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDRD1_MOUSE | Q99MV14b9w

(-) Related Entries Specified in the PDB File

4b9w STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1 IN COMPLEX WITH MILI PEPTIDE CONTAINING DIMETHYLARGININE 45.