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(-) Description

Title :  NMR STRUCTURE OF THE SECOND AND THIRD LOTUS DOMAINS OF TUDOR DOMAIN-CONTAINING PROTEIN 7 (NMR ENSEMBLE OVERLAY FOR LOTUS #3)
 
Authors :  G. Cui, M. Botuyan, G. Mer
Date :  10 Sep 12  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Tdrd7, Lotus Domain, Ost-Hth Domain, Rna Binding Domain, Germinal Granules, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Cui, M. Botuyan, G. Mer
Nmr Structure Of The Second And Third Lotus Domains Of Tudo Domain-Containing Protein 7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 7
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTEV
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLOTUS DOMAINS 2 AND 3
    GeneTDRD7, PCTAIRE2BP
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPCTAIRE2-BINDING PROTEIN, TUDOR REPEAT ASSOCIATOR WITH PCTAIRE 2, TRAP

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2LY2)

(-) Sites  (0, 0)

(no "Site" information available for 2LY2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LY2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LY2)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_OSTPS51644 OST-type HTH domain profile.TDRD7_MOUSE3-76
222-291
325-394
  2-
A:256-324
A:358-427
NMR Structure * (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_OSTPS51644 OST-type HTH domain profile.TDRD7_MOUSE3-76
222-291
325-394
  2-
A:256-324
A:358-427

(-) Exons   (0, 0)

(no "Exon" information available for 2LY2)

(-) 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:180
 aligned with TDRD7_MOUSE | Q8K1H1 from UniProtKB/Swiss-Prot  Length:1086

    Alignment length:180
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
          TDRD7_MOUSE   221 NKMDEVQNRIKEILDKHNNGIWISKLPHFYKEFYKEDLNQGVLQQFEHWPHICTVEKPCGGGQDSLLYPARREQPLKSDQDPEKELPPPPPAPKQEVPSQGSPAVMPDVKEKVAELLGKYSSGLWASALPKAFEDMYKVKFPEDALKNLASLSDVCTINYISGNTQKAILYAKLPLPTDK 400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..ee..hhhhhhhhhhh...hhhhhhhhhhh...eeee.........eeee.hhh......hhhhhh......hhhhh..........hhhhhhhhhhhhh....ee.hhhhhhhhhhhh...hhhhhhhhhhhhhheeeeee.....eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -HTH_OST  PDB: A:256-324 UniProt: 222-291                              ---------------------------------HTH_OST  PDB: A:358-427 UniProt: 325-394                              ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ly2 A  -2 GHMDEVQNRIKEILDKHNNGIWISKLPHFYKEFYKEDLNQGVLQQFEHWPHICTVEKPCGGGQDSLLYPARREQPLKSDQDPEKELPPPPPAPKQEVPSQGSPAVMPDVKEKVAELLGKYSSGLWASALPKAFEDMYKVKFPEDALKNLASLSDVCTINYISGNTQKAILYAKLPLPTDK 433
                             ||    263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
                             ||                                                                                                                                                                                 
                            -1|                                                                                                                                                                                 
                            256                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2LY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LY2)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (TDRD7_MOUSE | Q8K1H1)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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: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: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:0070306    lens fiber cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
    GO:0002089    lens morphogenesis in camera-type eye    The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
    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:0010608    posttranscriptional regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
    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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0035770    ribonucleoprotein granule    A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDRD7_MOUSE | Q8K1H12lh9 2ly1

(-) Related Entries Specified in the PDB File

2ly1