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(-) Description

Title :  CRYSTAL STRUCTURE OF TUDOR AND AUBERGINE [R13(ME2S)] COMPLEX
 
Authors :  H. P. Liu, Y. Huang, Z. Z. Li, W. M. Gong, R. M. Xu
Date :  05 Jul 10  (Deposition) - 15 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Tudor Domain, Ob-Fold, Germ Cell Formation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. P. Liu, J. Y. Wang, Y. Huang, Z. Z. Li, W. M. Gong, R. Lehmann, R. M. Xu
Structural Basis For Methylarginine-Dependent Recognition O Aubergine By Tudor
Genes Dev. V. 24 1876 2010
PubMed-ID: 20713507  |  Reference-DOI: 10.1101/GAD.1956010

(-) Compounds

Molecule 1 - MATERNAL PROTEIN TUDOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-SMT3
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTHE LAST EXTENDED TUDOR DOMAIN
    GeneTUD
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - PEPTIDE FROM AUBERGINE
    ChainsC
    EngineeredYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN DROSOPHILA.
    SynonymAUB[R13(ME2S)]
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
12MR1Mod. Amino AcidN3, N4-DIMETHYLARGININE

(-) Sites  (0, 0)

(no "Site" information available for 3NTH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NTH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.TUD_DROME455-513
641-696
1062-1122
1355-1414
1662-1718
1839-1898
2023-2082
2211-2269
2392-2451
  1-
-
-
-
-
-
-
-
A:2392-2451

(-) Exons   (0, 0)

(no "Exon" information available for 3NTH)

(-) 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:167
 aligned with TUD_DROME | P25823 from UniProtKB/Swiss-Prot  Length:2515

    Alignment length:167
                                  2356      2366      2376      2386      2396      2406      2416      2426      2436      2446      2456      2466      2476      2486      2496      2506       
           TUD_DROME   2347 ELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQE 2513
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains TUDOR-3nthA01 A:2347-2460                                                                                         ----------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.eeee.....eee....hhhhhhhhhhhhhhhhhhh..........eeeee......eeeeeeeee.....eeee......eeee..ee..hhhhh......eeee.hhhhh.....hhhhhhhhh.....eeeeeeee.....eeeeeee..ee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------TUDOR  PDB: A:2392-2451 UniProt: 2392-2451                  -------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nth A 2347 ELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQE 2513
                                  2356      2366      2376      2386      2396      2406      2416      2426      2436      2446      2456      2466      2476      2486      2496      2506       

Chain C from PDB  Type:PROTEIN  Length:6
 aligned with AUB_DROME | O76922 from UniProtKB/Swiss-Prot  Length:866

    Alignment length:6
           AUB_DROME     10 ARGRGR   15
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                3nth C   10 ARGrGR   15
                               |  
                               |  
                              13-2MR

   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  (0, 0)

(no "SCOP Domain" information available for 3NTH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (44, 50)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TUD_DROME | P25823)
molecular function
    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:0030719    P granule organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of polar granules, cytoplasmic, non-membranous RNA/protein complex aggregates in the primordial germ cells of many higher eukaryotes.
    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:0008298    intracellular mRNA localization    Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
    GO:0019090    mitochondrial rRNA export from mitochondrion    The directed movement of mitochondrial rRNA out of a mitochondrion.
    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:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0007277    pole cell development    The process whose specific outcome is the progression of the pole cell over time, from its formation to the mature structure.
    GO:0007278    pole cell fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a pole cell regardless of its environment; upon determination, the cell fate cannot be reversed.
    GO:0007315    pole plasm assembly    Establishment of the specialized cytoplasm found at the poles of the egg. An example of this is found in Drosophila melanogaster.
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: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: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.
    GO:0045495    pole plasm    Differentiated cytoplasm associated with a pole (animal, vegetal, anterior, or posterior) of an oocyte, egg or early embryo.

Chain C   (AUB_DROME | O76922)
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.
    GO:0034584    piRNA binding    Interacting selectively and non-covalently with a piRNA, a Piwi-associated RNA, a 24- to 30-nucleotide RNA derived from repeat or complex DNA sequence elements and processed by a Dicer-independent mechanism.
    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:0016246    RNA interference    The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes.
    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:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0046843    dorsal appendage formation    Establishment of the dorsal filaments, elaborate specializations of the chorion that protrude from the anterior end of the egg and facilitate embryonic respiration.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0030717    karyosome formation    The chromosome organization process in which meiotic chromosomes in the oocyte nucleus cluster together to form a compact spherical structure called the karyosome.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0046594    maintenance of pole plasm mRNA location    The process of maintaining mRNA in a specific location in the oocyte pole plasm. An example of this process is found in Drosophila melanogaster.
    GO:0007076    mitotic chromosome condensation    The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
    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:0010529    negative regulation of transposition    Any process that decreases the frequency, rate or extent of transposition. Transposition results in the movement of discrete segments of DNA between nonhomologous sites.
    GO:0001556    oocyte maturation    A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0007279    pole cell formation    Formation of a small group of cells (pole cells) at the posterior pole of the insect blastula. They are the first cells to cellularize after the arrival of nuclei at the end of the syncytial blastula stage and are the precursors to the insect germ cells.
    GO:0007318    pole plasm protein localization    Any process in which a protein is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0060213    positive regulation of nuclear-transcribed mRNA poly(A) tail shortening    Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
    GO:0046012    positive regulation of oskar mRNA translation    Any process that activates or increases the frequency, rate or extent of oskar mRNA translation.
    GO:0046011    regulation of oskar mRNA translation    Any process that modulates the frequency, rate or extent of oskar mRNA translation. To ensure the localization of Oskar protein at the posterior pole of the oocyte, translation of oskar mRNA is repressed during its transport to the posterior pole and activated upon localization of the mRNA at the posterior cortex.
    GO:0007317    regulation of pole plasm oskar mRNA localization    Any process that modulates the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    GO:0035282    segmentation    The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis.
    GO:0030423    targeting of mRNA for destruction involved in RNA interference    The process in which small interfering RNAs target cognate mRNA molecules for degradation.
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:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AUB_DROME | O769223nti
        TUD_DROME | P258233nti 3ntk 4q5w 4q5y

(-) Related Entries Specified in the PDB File

3nti 3ntk