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(-) Description

Title :  SOLUTION STRUCTURE OF THE UBA DOMAIN OF HUMAN TUDOR DOMAIN CONTAINING PROTEIN 3
 
Authors :  Y. O. Kamatari, N. Tochio, T. Nakanishi, K. Miyamoto, H. Li, N. Kobayashi, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 May 04  (Deposition) - 29 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Uba Domain, Tudor Domain Containing 3, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. O. Kamatari, N. Tochio, T. Nakanishi, K. Miyamoto, H. Li, N. Kobayashi, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Uba Domain Of Human Tudor Domain Containing Protein 3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TUDOR DOMAIN CONTAINING PROTEIN 3
    ChainsA
    EngineeredYES
    Expression System PlasmidP040301-26
    Expression System Vector TypePLASMID
    FragmentUBA DOMAIN
    GeneIMS CDNA CAE03871
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-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 1WJI)

(-) Sites  (0, 0)

(no "Site" information available for 1WJI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.TDRD3_HUMAN193-233  1A:8-47

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003778941dENSE00001475419chr13:60971122-6097114423TDRD3_HUMAN-00--
1.3bENST000003778943bENSE00002151362chr13:61013822-6101390685TDRD3_HUMAN-00--
1.4bENST000003778944bENSE00001423039chr13:61018821-6101888262TDRD3_HUMAN-00--
1.5aENST000003778945aENSE00002163556chr13:61034514-61034674161TDRD3_HUMAN1-25250--
1.6ENST000003778946ENSE00001205839chr13:61041372-61041513142TDRD3_HUMAN25-72480--
1.7ENST000003778947ENSE00001205834chr13:61057909-6105798072TDRD3_HUMAN73-96240--
1.9bENST000003778949bENSE00000923617chr13:61059933-61060082150TDRD3_HUMAN97-146500--
1.10ENST0000037789410ENSE00000923618chr13:61068569-61068709141TDRD3_HUMAN147-193471A:1-7 (gaps)18
1.11bENST0000037789411bENSE00000923619chr13:61083897-61084053157TDRD3_HUMAN194-246531A:8-5649
1.12ENST0000037789412ENSE00000923620chr13:61084764-61084889126TDRD3_HUMAN246-288431A:57-63 (gaps)16
1.13bENST0000037789413bENSE00000923621chr13:61102501-61103351851TDRD3_HUMAN288-5712840--
1.14aENST0000037789414aENSE00000923622chr13:61109242-61109367126TDRD3_HUMAN572-613420--
1.15ENST0000037789415ENSE00000923623chr13:61141659-61141784126TDRD3_HUMAN614-651380--
1.16cENST0000037789416cENSE00001475429chr13:61147750-61148011262TDRD3_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:63
 aligned with TDRD3_HUMAN | Q9H7E2 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:116
                                   176       186       196       206       216       226       236       246       256       266       276      
          TDRD3_HUMAN   167 GNRNREVLQKEKSTKSEGKHEGVYRELVDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGPPLRGRGKGRGRIRSEDEEDLGNARPSAPSTLFDFLESKMG 282
               SCOP domains d           1wjia_          A: Tudor domain containing protein 3, TDRD3                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------UBA-1wjiA01 A:8-44                   ---------------------------------------------------- Pfam domains
         Sec.struct. author .-----------......---------.hhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhh........------------------------......---------. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------UBA  PDB: A:8-47 UniProt: 193-233        ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:1-7 (gapsExon 1.11b  PDB: A:8-56 UniProt: 194-246 [INCOMPLETE]------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.12  PDB: A:57-63 (gaps)        Transcript 1 (2)
                 1wji A   1 G-----------SSGSSG---------VDEKALKHITEMGFSKEASRQALMDNGNNLEAALNVLLTSNKQKPVMGP------------------------PSGPSS---------G  63
                            |        -  |    | -       |10        20        30        40        50     |   -         -         -|    |   -     |
                            |           2    7         8                                              56                       57   62        63
                            1                                                                                                                   

   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  (0, 0)

(no "CATH Domain" information available for 1WJI)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: UBA (32)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (TDRD3_HUMAN | Q9H7E2)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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).
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
    GO:1903506    regulation of nucleic acid-templated transcription    Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0035145    exon-exon junction complex    A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDRD3_HUMAN | Q9H7E22lto 3pmt 3pnw 3s6w 5gvd 5gve

(-) Related Entries Specified in the PDB File

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