Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1 IN COMPLEX WITH MILI PEPTIDE CONTAINING DIMETHYLARGININE 45.
 
Authors :  N. Mathioudakis, A. Palencia, J. Kadlec, A. Round, K. Tripsianes, M. Sa R. S. Pillai, S. Cusack
Date :  08 Sep 12  (Deposition) - 17 Oct 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,P,S
Keywords :  Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Mathioudakis, A. Palencia, J. Kadlec, A. Round, K. Tripsianes, M. Sattler, R. S. Pillai, S. Cusack
The Multiple Tudor Domain-Containing Protein Tdrd1 Is A Molecular Scaffold For Mouse Piwi Proteins And Pirna Biogenesis Factors.
Rna V. 18 2056 2012
PubMed-ID: 22996915  |  Reference-DOI: 10.1261/RNA.034181.112

(-) Compounds

Molecule 1 - TUDOR DOMAIN-CONTAINING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PETM11
    Expression System Vector Type: PLASMID
    Fragment: EXTENDED TUDOR DOMAIN TD3, RESIDUES 692-892
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TDRD1
 
Molecule 2 - PIWI-LIKE PROTEIN 2
    Chains: P, S
    Fragment: N-TERMINAL PEPTIDE CONTAINING METHYLATED ARG45, RESIDUES 38-50
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ARG45 IS SYMMETRICALLY DIMETHYLATED
    Synonym: MILI
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABPS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
12MR2Mod. Amino AcidN3, N4-DIMETHYLARGININE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL B:714 , CYS B:715 , MET B:716 , MET B:717 , GLN B:843 , 2MR S:45 , LEU S:47BINDING SITE FOR RESIDUE GOL B1893
2AC2SOFTWARECYS A:715 , MET A:717 , GLN A:843 , 2MR P:45 , LEU P:47BINDING SITE FOR RESIDUE GOL A1893

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B9W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:750 -Pro A:751

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B9W)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUDORPS50304 Tudor domain profile.TDRD1_MOUSE307-367
536-595
756-815
 
982-1040		  2-
-
A:756-815
B:756-815
-

(-) Exons   (0, 0)

(no "Exon" information available for 4B9W)

(-) 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:196
 aligned with TDRD1_MOUSE | Q99MV1 from UniProtKB/Swiss-Prot  Length:1172

    Alignment length:196
                                   706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      
          TDRD1_MOUSE   697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhhhh............eeeee......eeeeeeeee.....eeeee.....eeeehhh.eee.hhhhhh.....eeeee..ee......hhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........hhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------TUDOR  PDB: A:756-815 UniProt: 756-815                      ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9w A 697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
                                   706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with TDRD1_MOUSE | Q99MV1 from UniProtKB/Swiss-Prot  Length:1172

    Alignment length:196
                                   706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886      
          TDRD1_MOUSE   697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQKPPNGFKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeee..eeeeee...hhhhhhhhhhhhhhhhhh.-----.......eeeee......eeeeeeeee.....eeeee.....eeeehhh.ee..hhhhhh.....eeeee..ee......hhhhhhhhhhhhh...eeeeeeee....eeeeeee........hhhhhhhh...ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------TUDOR  PDB: B:756-815 UniProt: 756-815                      ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b9w B 697 LEWTWVEFTVDETVDVVVCMMYSPGEFYCHFLKDDALEKLDDLNQSLADYCAQ-----FKAEIGRPCCAFFSGDGNWYRALVKEILPSGNVKVHFVDYGNVEEVTTDQLQAILPQFLLLPFQGMQCWLVDIQPPNKHWTKEATARFQACVVGLKLQARVVEITANGVGVELTDLSTPYPKIISDVLIREQLVLRCG 892
                                   706       716       726       736       746  |    756       766       776       786       796       806       816       826       836       846       856       866       876       886      
                                                                              749   755                                                                                                                                         


Chain P from PDB  Type:PROTEIN  Length:8
 aligned with PIWL2_MOUSE | Q8CDG1 from UniProtKB/Swiss-Prot  Length:971

    Alignment length:8
          PIWL2_MOUSE    43 AGRGLVFR  50
               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
                 4b9w P  43 AGrGLVFR  50
                              |     
                              |     
                             45-2MR 


Chain S from PDB  Type:PROTEIN  Length:8
 aligned with PIWL2_MOUSE | Q8CDG1 from UniProtKB/Swiss-Prot  Length:971

    Alignment length:8
          PIWL2_MOUSE    43 AGRGLVFR  50
               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
                 4b9w S  43 AGrGLVFR  50
                              |     
                             45-2MR
   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 4B9W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B9W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B9W)

(-) Gene Ontology  (32, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TDRD1_MOUSE | Q99MV1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    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:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    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: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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    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.

Chain P,S   (PIWL2_MOUSE | Q8CDG1)
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: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: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:0000966    RNA 5'-end processing    Any process involved in forming the mature 5' end of an RNA molecule.
    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:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0030718    germ-line stem cell population maintenance    Any process by which an organism or tissue maintains a population of germ-line stem cells.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    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: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:0071442    positive regulation of histone H3-K14 acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
    GO:2000617    positive regulation of histone H3-K9 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0060903    positive regulation of meiosis I    Any process that increases the rate, frequency, or extent of meiosis I, a cell cycle process comprising the steps by which a cell progresses through the first phase of meiosis, in which cells divide and homologous chromosomes are paired and segregated from each other, producing two daughter cells.
    GO:0045727    positive regulation of translation    Any process that activates or increases 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: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: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:1990923    PET complex    A protein complex that is composed of at least EXD1, TDRD12 and some PIWI protein. The complex is required for MILI slicing-triggered biogenesis and loading of MIWI2 piRNAs
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0097433    dense body    An electron dense body which may contain granules.
    GO:0010370    perinucleolar chromocenter    A chromocenter adjacent to the nucleolus.
    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:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    2MR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:750 - Pro A:751   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4b9w
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PIWL2_MOUSE | Q8CDG1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TDRD1_MOUSE | Q99MV1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PIWL2_MOUSE | Q8CDG1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TDRD1_MOUSE | Q99MV1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TDRD1_MOUSE | Q99MV1: 4b9x

(-) Related Entries Specified in the PDB File

4b9x STRUCTURE OF EXTENDED TUDOR DOMAIN TD3 FROM MOUSE TDRD1