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(-) Description

Title :  SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF TUDOR AND KH DOMAIN CONTAINING PROTEIN
 
Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Tudor Domain, Tudor And Kh Domain Containing Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Tudor Domain Of Tudor And Kh Domain Containing Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TUDOR AND KH DOMAIN-CONTAINING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050905-13
    Expression System Vector Type: PLASMID
    Fragment: TUDOR DOMAIN
    Gene: TDRKH, TDRD2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DIQ)

(-) Sites  (0, 0)

(no "Site" information available for 2DIQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DIQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DIQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DIQ)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.TDRKH_HUMAN353-412  1A:32-91

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003688272bENSE00001941603chr1:151762998-151762856143TDRKH_HUMAN-00--
1.4bENST000003688274bENSE00002159845chr1:151755525-151755375151TDRKH_HUMAN1-42420--
1.6ENST000003688276ENSE00001296403chr1:151754063-151753957107TDRKH_HUMAN42-77360--
1.7eENST000003688277eENSE00001311108chr1:151752616-151752427190TDRKH_HUMAN78-141640--
1.8aENST000003688278aENSE00001325745chr1:151751718-151751579140TDRKH_HUMAN141-187470--
1.9aENST000003688279aENSE00001300321chr1:151751482-151751161322TDRKH_HUMAN188-2951081A:1-22
1.10ENST0000036882710ENSE00001294518chr1:151749075-151748915161TDRKH_HUMAN295-348541A:3-27 (gaps)36
1.11ENST0000036882711ENSE00001311139chr1:151748744-151748572173TDRKH_HUMAN349-406581A:28-8558
1.12ENST0000036882712ENSE00001317063chr1:151748360-15174829665TDRKH_HUMAN406-428231A:85-106 (gaps)23
1.13ENST0000036882713ENSE00001316963chr1:151748019-151747868152TDRKH_HUMAN428-478511A:106-110 (gaps)50
1.14ENST0000036882714ENSE00001307144chr1:151747642-151747541102TDRKH_HUMAN479-512340--
1.15ENST0000036882715ENSE00001291350chr1:151747282-15174718697TDRKH_HUMAN513-545330--
1.16aENST0000036882716aENSE00001325167chr1:151746980-15174688992TDRKH_HUMAN545-561170--
1.17ENST0000036882717ENSE00001419045chr1:151744462-151744040423TDRKH_HUMAN-00--

(-) 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:110
 aligned with TDRKH_HUMAN | Q9Y2W6 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:209
                                   278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468         
          TDRKH_HUMAN   269 GSWEKPSDDSFQKSEAQAIPEMPMFEIPSPDFSFHADEYLEVYVSASEHPNHFWIQIVGSRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEALDEFDRLTHCADWKPLVAKISSYVQTGISTWPKIYLYDTSNG 477
               SCOP domains ------------------------------------------------------------d2diqa1 A:8-104 Tudor and KH domain-containing protein TDRKH                                     ---------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------------------------....-----------...hhhhhhhhhhhhhh..............eeee........eeeee........eeeee.....eeee.hhh.ee..hhhh...............-..---------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------TUDOR  PDB: A:32-91 UniProt: 353-412                        ----------------------------------------------------------------- PROSITE
           Transcript 1 (1) --------------------------Exon 1.10  PDB: A:3-27 (gaps) UniProt: 295-348        Exon 1.11  PDB: A:28-85 UniProt: 349-406                  ---------------------Exon 1.13  PDB: A:106-110 (gaps) UniProt: 428-478  Transcript 1 (1)
           Transcript 1 (2) Exon 1.9a  PDB: A:1-2      --------------------------------------------------------------------------------------------------------------Exon 1.12              ------------------------------------------------- Transcript 1 (2)
                 2diq A   1 GS------------------------------------------SGSS-----------GRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIA-SG---------------------------------------------PSSG 110
                             |       -         -         -         -    |  | -         7        17        27        37        47        57        67        77        87        97      |106         -         -         -         -     |   
                             2                                          3  6           7                                                                                              104 ||                                           107   
                                                                                                                                                                                        105|                                                 
                                                                                                                                                                                         106
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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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DIQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DIQ)

(-) Gene Ontology  (13, 13)

NMR Structure(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

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UniProtKB/Swiss-Prot
        TDRKH_HUMAN | Q9Y2W6: 3fdr 5j39

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