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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Authors :  M. F Amaya, M. A. Adams, Y. Guo, Y. Li, I. Kozieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, C. Bountra, A. Bochkarev, J. Min, Structural Genomics Consortium (Sgc)
Date :  26 Nov 08  (Deposition) - 06 Jan 09  (Release) - 15 Dec 09  (Revision)
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Tdrd2, Tudor, Structural Genomics, Structural Genomics Consortium, Sgc, Alternative Splicing, Rna-Binding, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  C. Chen, J. Jin, D. A. James, M. A. Adams-Cioaba, J. G. Park, Y. Guo, E. Tenaglia, C. Xu, G. Gish, J. Min, T. Pawson
Mouse Piwi Interactome Identifies Binding Mechanism Of Tdrkh Tudor Domain To Arginine Methylated Miwi
Proc. Natl. Acad. Sci. Usa V. 106 20336 2009
PubMed-ID: 19918066  |  Reference-DOI: 10.1073/PNAS.0911640106
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTUDOR DOMAIN
    GeneTDRKH, TDRD2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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 3FDR)

(-) Sites  (0, 0)

(no "Site" information available for 3FDR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FDR)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FDR)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1TUDORPS50304 Tudor domain profile.TDRKH_HUMAN353-412  1A:27-86

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:89
 aligned with TDRKH_HUMAN | Q9Y2W6 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:89
                                   340       350       360       370       380       390       400       410         
               SCOP domains d3fdra_ A: Tudor and KH domain-containing protein TDRKH                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.............eeeee......eeeeeeeee.....eeeee.....eeeehhhhhee.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------TUDOR  PDB: A:27-86 UniProt: 353-412                        ------- PROSITE
           Transcript 1 (1) Exon 1.10         Exon 1.11  PDB: A:23-80 UniProt: 349-406                  ------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------Exon 1.12      Transcript 1 (2)
                                    14        24        34        44        54        64        74        84         

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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FDR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FDR)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TDRKH_HUMAN | Q9Y2W6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
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:0009566    fertilization    The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0007140    male meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.
    GO:0071547    piP-body    A P granule that contains the PIWIL4-TDRD9 module, a set of proteins that act in the secondary piRNA pathway.


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 Related Entries

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

        TDRKH_HUMAN | Q9Y2W62diq 5j39

(-) Related Entries Specified in the PDB File

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