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(-) Description

Title :  COMPLEX STRUCTURE OF THE MIWI PAZ DOMAIN BOUND TO METHYLATED SINGLE STRANDED RNA
 
Authors :  B. Simon, J. P. Kirkpatrick, S. Eckhardt, P. Sehr, M. A. Andrade-Navarr R. S. Pillai, T. Carlomagno
Date :  27 May 10  (Deposition) - 26 Jan 11  (Release) - 26 Oct 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Rna-Protein Complex, Differentiation, Rna Interference (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Simon, J. P. Kirkpatrick, S. Eckhardt, M. Reuter, E. A. Rocha, M. A. Andrade-Navarro, P. Sehr, R. S. Pillai, T. Carlomagno
Recognition Of 2'-O-Methylated 3'-End Of Pirna By The Paz Domain Of A Piwi Protein.
Structure V. 19 172 2011
PubMed-ID: 21237665  |  Reference-DOI: 10.1016/J.STR.2010.11.015

(-) Compounds

Molecule 1 - PIWI-LIKE PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPAZ-DOMAIN, RESIDUES 276-425
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMIWI
 
Molecule 2 - 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'
    ChainsB
    Other DetailsRNA WITH 3'-TERMINAL O2'-METHYL URIDINE
    Other Details - SourceBASED ON BIOLOGICAL SEQUENCE
    SynonymPIRNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2XFM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL1_MOUSE278-392  1A:278-392
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL1_MOUSE278-392  1A:278-392

(-) Exons   (0, 0)

(no "Exon" information available for 2XFM)

(-) 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:120
 aligned with PIWL1_MOUSE | Q9JMB7 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:120
                                   285       295       305       315       325       335       345       355       365       375       385       395
          PIWL1_MOUSE   276 RSETVLDFMFNLYQQTEEHKFQEQVSKELIGLIVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLTD 395
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --PAZ-2xfmA01 A:278-395                                                                                                  Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeee..eee.................hhhhhhhh............eeee...............eeehhh.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --PAZ  PDB: A:278-392 UniProt: 278-392                                                                               --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xfm A 276 RSETVLDFMFNLYQQTEEHKFQEQVSKELIGLIVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLTD 395
                                   285       295       305       315       325       335       345       355       365       375       385       395

Chain B from PDB  Type:RNA  Length:8
                                        
                 2xfm B   1 ACCGACUu   8
                                   |
                                   8-OMU

   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 2XFM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (PIWL1_MOUSE | Q9JMB7)
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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
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:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    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: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:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    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:0097433    dense body    An electron dense body which may contain granules.
    GO:0005845    mRNA cap binding complex    Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
    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: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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        PIWL1_MOUSE | Q9JMB74p1z

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