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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HILI PAZ DOMAIN
 
Authors :  Y. Tian, D. K. Simanshu, J. -B. Ma, D. J. Patel
Date :  01 Aug 10  (Deposition) - 12 Jan 11  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D  (2x)
Keywords :  Piwi, Rna Silencing, Pi-Rna, Hiwi1, Hili, Paz Domain, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tian, D. K. Simanshu, J. B. Ma, D. J. Patel
Inaugural Article: Structural Basis For Pirna 2'-O-Methylated 3'-End Recognition By Piwi Paz (Piwi/Argonaute/Zwille) Domains.
Proc. Natl. Acad. Sci. Usa V. 108 903 2011
PubMed-ID: 21193640  |  Reference-DOI: 10.1073/PNAS.1017762108

(-) Compounds

Molecule 1 - PIWI-LIKE PROTEIN 2
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPAZ DOMAIN (UNP RESIDUES 389-525)
    GenePIWIL2, HILI
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCANCER/TESTIS ANTIGEN 80, CT80

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)A   
Biological Unit 2 (1x) BC 
Biological Unit 3 (2x)   D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3O7X)

(-) Sites  (0, 0)

(no "Site" information available for 3O7X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O7X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O7X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O7X)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL2_HUMAN417-496
 
 
 
  4A:417-496
B:417-496
C:417-496
D:417-496
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL2_HUMAN417-496
 
 
 
  2A:417-496
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL2_HUMAN417-496
 
 
 
  2-
B:417-496
C:417-496
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL2_HUMAN417-496
 
 
 
  2-
-
-
D:417-496

(-) Exons   (0, 0)

(no "Exon" information available for 3O7X)

(-) 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:116
 aligned with PIWL2_HUMAN | Q8TC59 from UniProtKB/Swiss-Prot  Length:973

    Alignment length:116
                                   395       405       415       425       435       445       455       465       475       485       495      
          PIWL2_HUMAN   386 RNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMT 501
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhh..ee..eee.......eee.....eeehhhhhhhhh..........eeee................eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PAZ  PDB: A:417-496 UniProt: 417-496                                            ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3o7x A 386 SNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMT 501
                                   395       405       415       425       435       445       455       465       475       485       495      

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with PIWL2_HUMAN | Q8TC59 from UniProtKB/Swiss-Prot  Length:973

    Alignment length:116
                                   395       405       415       425       435       445       455       465       475       485       495      
          PIWL2_HUMAN   386 RNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMT 501
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhh..ee..eee.......eee.....eeehhhhhhhhh..........eeee..------------..eee....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PAZ  PDB: B:417-496 UniProt: 417-496                                            ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3o7x B 386 SNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRP------------GEILLLPELSFMT 501
                                   395       405       415       425       435       445       455       465       475|        -   |   495      
                                                                                                                    476          489            

Chain C from PDB  Type:PROTEIN  Length:107
 aligned with PIWL2_HUMAN | Q8TC59 from UniProtKB/Swiss-Prot  Length:973

    Alignment length:116
                                   395       405       415       425       435       445       455       465       475       485       495      
          PIWL2_HUMAN   386 RNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMT 501
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhh..ee..eee.......eee.....eeehhhhhhhhh..........eeee....---------...eee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PAZ  PDB: C:417-496 UniProt: 417-496                                            ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3o7x C 386 SNDCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSE---------KGEILLLPELSFMT 501
                                   395       405       415       425       435       445       455       465       475  |      -  |    495      
                                                                                                                      478       488             

Chain D from PDB  Type:PROTEIN  Length:110
 aligned with PIWL2_HUMAN | Q8TC59 from UniProtKB/Swiss-Prot  Length:973

    Alignment length:114
                                   397       407       417       427       437       447       457       467       477       487       497    
          PIWL2_HUMAN   388 DCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSFMT 501
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) PAZ-3o7xD01 D:388-501                                                                                              Pfam domains (1)
           Pfam domains (2) PAZ-3o7xD02 D:388-501                                                                                              Pfam domains (2)
           Pfam domains (3) PAZ-3o7xD03 D:388-501                                                                                              Pfam domains (3)
           Pfam domains (4) PAZ-3o7xD04 D:388-501                                                                                              Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhh..ee..eee.......eee.....eeehhhhhhhhh..........eeee.......----.....eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------PAZ  PDB: D:417-496 UniProt: 417-496                                            ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3o7x D 388 DCVLDVMHAIYQQNKEHFQDECTKLLVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDGKEITFLEYYSKNYGITVKEEDQPLLIHRPSERQD----LLKGEILLLPELSFMT 501
                                   397       407       417       427       437       447       457       467       477   |   487       497    
                                                                                                                       481  486               

   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 3O7X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O7X)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Family: PAZ (14)
1aPAZ-3o7xD01D:388-501
1bPAZ-3o7xD02D:388-501
1cPAZ-3o7xD03D:388-501
1dPAZ-3o7xD04D:388-501

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PIWL2_HUMAN | Q8TC59)
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.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIWL2_HUMAN | Q8TC593qir

(-) Related Entries Specified in the PDB File

3o3i CRYSTAL STRUCTURE OF HUMAN HIWI1 PAZ DOMAIN (RESIDUES 277- 399) IN COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OH AT ITS 3'-END
3o6e CRYSTAL STRUCTURE OF HUMAN HIWI1 PAZ DOMAIN (RESIDUES 277- 399) IN COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OCH3 AT ITS 3'-END
3o7v CRYSTAL STRUCTURE OF HUMAN HIWI1 (V361M) PAZ DOMAIN (RESIDUES 277-399) IN COMPLEX WITH 14-MER RNA (12-BP + 2-NT OVERHANG) CONTAINING 2'-OCH3 AT ITS 3'-END