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(-) Description

Title :  CRYSTAL STRUCTURE OF TUDOR
 
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 :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3NTK)

(-) Sites  (0, 0)

(no "Site" information available for 3NTK)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:2466 -A:2514
2B:2466 -B:2514

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 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
 
  2-
-
-
-
-
-
-
-
A:2392-2451
B:2392-2451
Biological Unit 1 (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
-
Biological Unit 2 (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-
-
-
-
-
-
-
-
-
B:2392-2451

(-) Exons   (0, 0)

(no "Exon" information available for 3NTK)

(-) Sequences/Alignments

Asymmetric 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:169
 aligned with TUD_DROME | P25823 from UniProtKB/Swiss-Prot  Length:2515

    Alignment length:169
                                  2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505         
           TUD_DROME   2346 AELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQEC 2514
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhh..........eeeee......eeeeeeeee.....eeee......eeee..ee..hhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee..eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------TUDOR  PDB: A:2392-2451 UniProt: 2392-2451                  --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ntk A 2346 AELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQEC 2514
                                  2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505         

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with TUD_DROME | P25823 from UniProtKB/Swiss-Prot  Length:2515

    Alignment length:169
                                  2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505         
           TUD_DROME   2346 AELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKCDAALLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQEC 2514
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TUDOR-3ntkB01 B:2346-2460                                                                                          ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) TUDOR-3ntkB02 B:2346-2460                                                                                          ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhh..........eeeee......eeeeeeeee.....eeee......eeee..ee..hhhhhh.....eeeeehhhhhhhh---hhhhh.......eeeeeeeee.....eeeeeee..eehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------TUDOR  PDB: B:2392-2451 UniProt: 2392-2451                  --------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ntk B 2346 AELHNCVVVQFDGPMSFYVQMESDVPALEQMTDKLLDAEQDLPAFSDLKEGALCVAQFPEDEVFYRAQIRKVLDDGKCEVHFIDFGNNAVTQQFRQLPEELAKPARYSRHCELDASTISKC---LLQSFIDTRFSETFQVEILATKGTGTHVVRLFYQSKNISEKLQEC 2514
                                  2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465|   | 2475      2485      2495      2505         
                                                                                                                                                 2466   |                                            
                                                                                                                                                     2470                                            

   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 3NTK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TUD_DROME | P258233nth 3nti 4q5w 4q5y

(-) Related Entries Specified in the PDB File

3nth 3nti