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(-) Description

Title :  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
 
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 :  2.10
Chains :  Asym. Unit :  A,X
Biol. Unit 1:  A,X  (2x)
Keywords :  Piwi, Rna Silencing, Pi-Rna, Hiwi1, Hili, Paz Domain, Rna Binding Protein, Rna Binding Protein-Rna Complex (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 1
    ChainsX
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPAZ DOMAIN (UNP RESIDUES 276-399)
    GeneHIWI, PIWI-LIKE PROTEIN 1, PIWIL1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))- 3')
    ChainsA
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AX
Biological Unit 1 (2x)AX

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2OMU1Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2OMU2Mod. NucleotideO2'-METHYLURIDINE 5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 3O7V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O7V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O7V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O7V)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL1_HUMAN277-391  1X:277-391
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PAZPS50821 PAZ domain profile.PIWL1_HUMAN277-391  2X:277-391

(-) Exons   (0, 0)

(no "Exon" information available for 3O7V)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:14
                                              
                 3o7v A   1 GCGAAUAUUCGCUu  14
                                    10   |
                                        14-OMU

Chain X from PDB  Type:PROTEIN  Length:107
 aligned with PIWL1_HUMAN | Q96J94 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:117
                                   286       296       306       316       326       336       346       356       366       376       386       
          PIWL1_HUMAN   277 ETVLDFMFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGPAMLIPELCYLTGLT 393
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains PAZ-3o7vX01 X:277-393                                                                                                 Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhhhhhhhhhhh..eeee.....eee..eee.......eee.....eeehhhhhhhhhh.........eeee...----------..eeehhh.ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PAZ  PDB: X:277-391 UniProt: 277-391                                                                               -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3o7v X 277 ETVLDFmFNFYHQTEEHKFQEQVSKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADGSEVSFLEYYRKQYNQEITDLKQPmLVSQPK----------GPAmLIPELCYLTGLT 393
                                  |286       296       306       316       326       336       346       356    |  366|        - |  |  386       
                                  |                                                                           361-MSE67        378  |            
                                283-MSE                                                                                           381-MSE        

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  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 3O7V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O7V)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain X   (PIWL1_HUMAN | Q96J94)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PIWL1_HUMAN | Q96J942l5c 2l5d 3o3i 3o6e

(-) 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
3o7x CRYSTAL STRUCTURE OF HUMAN HILI PAZ DOMAIN (RESIDUES 277- 399)