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(-) Description

Title :  STRUCTURE OF TRBP2 AND ITS MOLECULE IMPLICATIONS FOR MIRNA PROCESSING
 
Authors :  Y. A. Yuan, H. Y. Chen
Date :  22 Jan 10  (Deposition) - 26 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Trbp2, Mirna Processing, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. W. Yang, H. Y. Chen, J. Yang, S. Machida, N. H. Chua, Y. A. Yuan
Structure Of Arabidopsis Hyponastic Leaves1 And Its Molecular Implications For Mirna Processing
Structure V. 18 594 2010
PubMed-ID: 20462493  |  Reference-DOI: 10.1016/J.STR.2010.02.006

(-) Compounds

Molecule 1 - RISC-LOADING COMPLEX SUBUNIT TARBP2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDRBM 2 DOMAIN, UNP RESIDUES 161-231
    GeneTARBP2, TRBP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTAR RNA-BINDING PROTEIN 2, TRANS-ACTIVATION-RESPONSIVE RNA- BINDING PROTEIN
 
Molecule 2 - RNA (5'-R(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3')
    ChainsB, C
    EngineeredYES
    Other DetailsSYNTHETIC RNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3ADL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.TRBP2_HUMAN30-97
159-227
298-361
  1-
A:161-227
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002669871bENSE00000938709chr12:53894705-53895245541TRBP2_HUMAN1-18180--
1.3aENST000002669873aENSE00001767359chr12:53895799-53895968170TRBP2_HUMAN18-75580--
1.4ENST000002669874ENSE00001148574chr12:53896811-53896913103TRBP2_HUMAN75-109350--
1.5ENST000002669875ENSE00001148567chr12:53897497-5389759296TRBP2_HUMAN109-141330--
1.6ENST000002669876ENSE00001148561chr12:53898181-5389825373TRBP2_HUMAN141-165251A:152-165 (gaps)16
1.7ENST000002669877ENSE00001148552chr12:53898482-53898599118TRBP2_HUMAN166-205401A:166-20540
1.8ENST000002669878ENSE00001148544chr12:53898919-53899046128TRBP2_HUMAN205-247431A:205-22723
1.9ENST000002669879ENSE00001148535chr12:53899433-53899634202TRBP2_HUMAN248-315680--
1.10bENST0000026698710bENSE00000938717chr12:53899775-53900213439TRBP2_HUMAN315-366520--

(-) 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:76
 aligned with TRBP2_HUMAN | Q15633 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:78
                                   159       169       179       189       199       209       219        
          TRBP2_HUMAN   150 PVSPQQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHT 227
               SCOP domains d3adla_   A: automated matches                                                 SCOP domains
               CATH domains -----3a  dlA01 A:157-227  [code=3.30.160.20, no name defined]                  CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......--hhhhhhhhhhhhh.....eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------DS_RBD  PDB: A:161-227 UniProt: 159-227                               PROSITE
           Transcript 1 (1) Exon 1.6        Exon 1.7  PDB: A:166-205                ---------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.8  PDB: A:205-22 Transcript 1 (2)
                 3adl A 152 GLVPRGS--HEVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHT 227
                                  |159       169       179       189       199       209       219        
                                158  |                                                                    
                                   159                                                                    

Chain B from PDB  Type:RNA  Length:10
                                          
                 3adl B   1 CGCGCGCGCG  10
                                    10

Chain C from PDB  Type:RNA  Length:10
                                          
                 3adl C   1 CGCGCGCGCG  10
                                    10

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ADL)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRBP2_HUMAN | Q15633)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0035198    miRNA binding    Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
    GO:0036002    pre-mRNA binding    Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a mRNA molecule.
    GO:0070883    pre-miRNA binding    Interacting selectively and non-covalently with a precursor microRNA (pre-miRNA) transcript, a stem-loop-containing precursor of microRNA.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0035197    siRNA binding    Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme.
biological process
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0035280    miRNA loading onto RISC involved in gene silencing by miRNA    The transfer of a microRNA (miRNA) strand from a miRNA:miRNA duplex onto the RNA-initiated silencing complex (RISC).
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0050689    negative regulation of defense response to virus by host    Any host process that results in the inhibition of antiviral immune response mechanisms, thereby facilitating viral replication. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    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:0045070    positive regulation of viral genome replication    Any process that activates or increases the frequency, rate or extent of viral genome replication.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0035196    production of miRNAs involved in gene silencing by miRNA    Cleavage of stem-loop RNA precursors into microRNAs (miRNAs), a class of small RNAs that primarily silence genes by blocking the translation of mRNA transcripts into protein.
    GO:0030422    production of siRNA involved in RNA interference    Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
    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:0046782    regulation of viral transcription    Any process that modulates the frequency, rate or extent of the transcription of the viral genome.
    GO:0035087    siRNA loading onto RISC involved in RNA interference    The transfer of small interfering RNA molecules (siRNAs) from the Dicer family of enzymes that cleave the double-stranded RNA, onto the nuclease-containing RNA-initiated silencing complex (RISC), in the context of RNA interference.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
    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:0030423    targeting of mRNA for destruction involved in RNA interference    The process in which small interfering RNAs target cognate mRNA molecules for degradation.
cellular component
    GO:0016442    RISC complex    A ribonucleoprotein complex that contains members of the Argonaute family of proteins, small interfering RNAs (siRNAs) or microRNAs (miRNAs), and miRNA or siRNA-complementary mRNAs, in addition to a number of accessory factors. The RISC complex is involved in posttranscriptional repression of gene expression through downregulation of translation or induction of mRNA degradation.
    GO:0070578    RISC-loading complex    A trimeric protein complex required for the formation of a mature RNA-induced silencing complex (RISC). In humans the complex is composed of the endonuclease Dicer (DICER1), TRBP (TARBP2) and the Argonaute protein Ago2 (EIF2C2/AGO2). Within the complex, Dicer and TRBP are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto Ago2. Ago2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from Dicer and TRBP. This complex has endoribonuclease activity.
    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:0035068    micro-ribonucleoprotein complex    A complex containing both protein and micro-RNA (miRNA) molecules. miRNAs are approximately 22 nucleotide noncoding RNAs derived from endogenous genes; they are processed from the stem of a longer hairpin like structure termed a pre-miRNA.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRBP2_HUMAN | Q156332cpn 3llh 4wyq

(-) Related Entries Specified in the PDB File

3adg 3adi 3adj